Contacts of the helix formed by residues 320 - 342 (chain A) in PDB entry 1QI9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 320 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 3.7 35.2 - - + -
297A PHE* 3.8 6.5 - - + -
298A ASN 5.3 0.2 + - - -
299A ARG* 4.0 33.6 + - + +
315A PHE* 3.6 21.3 + - + -
319A GLY* 1.4 70.3 - - - -
321A SER* 1.3 64.5 + - - +
323A TYR* 3.8 6.5 - - - -
324A PHE* 3.0 30.9 + - + -
278B ASP 5.0 1.3 - - - +
279B ASN* 3.6 21.5 - - - +
280B ILE* 3.3 23.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A PHE* 3.3 30.8 + - - -
316A VAL* 3.8 16.1 + - - +
319A GLY 3.1 0.8 + - - -
320A ILE* 1.3 80.9 - - - +
322A HIS* 1.4 62.3 + - - +
325A ARG* 3.0 30.1 + - - +
280B ILE* 3.5 10.8 - - - -
331B GLU* 2.6 32.6 + - - +
334B GLN* 3.9 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A PHE 3.3 1.4 + - - -
316A VAL 3.4 17.0 + - - +
317A ASN* 3.6 1.4 - - - -
318A PHE* 2.9 29.9 + + - +
319A GLY 2.8 10.6 + - - +
321A SER* 1.4 81.3 - - - +
323A TYR* 1.4 63.6 + - - +
325A ARG* 3.6 19.6 + - - +
326A LEU* 3.2 45.0 + - + +
432A LEU* 3.6 15.8 - - + +
509A GLU* 4.2 2.0 + - - +
513A PHE* 3.8 28.0 - + - -
519A PHE* 3.8 28.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ALA* 2.7 44.4 + - + -
291A LEU* 3.6 15.4 - - - +
292A LEU* 3.8 8.6 + - + -
297A PHE* 3.6 46.5 - + + +
319A GLY 3.0 10.3 + - - +
320A ILE* 3.7 6.3 - - + +
321A SER 3.3 0.2 - - - -
322A HIS* 1.4 80.3 - - - +
324A PHE* 1.4 90.0 + + - +
326A LEU* 3.4 2.3 + - - +
327A ILE* 3.1 27.1 + - + +
428A VAL* 4.3 1.3 - - + +
429A LEU* 3.6 26.3 - - + +
432A LEU* 3.3 31.6 - - + +
433A ILE* 4.7 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A TYR* 3.7 36.0 - + - -
288A ALA* 4.2 19.1 - - + -
289A LEU* 3.8 28.3 - - + -
292A LEU* 4.2 11.2 - - + -
320A ILE* 3.0 28.6 + - + +
323A TYR* 1.4 98.5 - + - +
325A ARG* 1.3 66.4 + - - +
327A ILE* 3.4 14.4 + - + +
328A GLY 3.5 7.3 + - - -
279B ASN* 3.6 22.2 - - + -
280B ILE* 3.8 27.1 - - + -
281B ASN* 4.0 11.7 + - - +
328B GLY* 3.9 9.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A VAL* 5.0 6.9 + - - +
321A SER* 3.0 23.0 + - - +
322A HIS* 3.6 26.7 + - - +
323A TYR 3.2 0.2 - - - -
324A PHE* 1.3 78.4 - - - +
326A LEU* 1.3 69.2 + - - +
328A GLY 3.4 0.9 + - - -
329A ALA* 2.8 30.4 + - + +
509A GLU* 2.9 43.4 + - - -
513A PHE* 5.1 2.8 - - - -
328B GLY 3.3 26.0 - - - +
329B ALA* 4.1 7.6 + - - +
331B GLU* 3.8 11.9 - - + +
332B LEU* 3.6 48.8 - - - +
335B ARG* 4.6 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A HIS* 3.2 42.7 + - + +
325A ARG* 1.3 90.7 - - - +
327A ILE* 1.3 61.5 + - - +
328A GLY 3.1 1.8 - - - -
329A ALA* 4.0 12.3 - - + +
330A ALA* 2.7 37.4 + - + +
428A VAL* 3.7 27.8 - - + -
432A LEU* 4.7 3.4 - - + -
505A THR* 5.2 10.1 - - + -
506A LEU* 3.8 27.6 - - + -
509A GLU* 3.7 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ASN* 3.0 30.6 + - + +
284A ALA* 5.0 3.1 - - + -
285A TYR* 4.1 30.7 - - + +
288A ALA* 4.6 9.4 - - + -
323A TYR* 3.1 25.8 + - + +
324A PHE* 3.7 11.2 - - + +
325A ARG 3.3 0.2 - - - -
326A LEU* 1.3 75.1 - - - +
328A GLY* 1.3 57.8 + - - +
425A PHE* 3.1 39.7 - - + +
428A VAL* 4.0 12.3 - - + -
429A LEU* 3.8 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ASN* 3.6 13.0 - - - +
324A PHE 3.5 4.8 + - - -
325A ARG 3.4 5.4 + - - -
326A LEU 3.1 0.2 - - - -
327A ILE* 1.3 77.9 - - - +
329A ALA* 1.3 63.6 + - - +
330A ALA 3.2 2.2 - - - -
331A GLU* 3.1 23.2 + - - +
324B PHE 3.9 6.7 - - - -
325B ARG* 3.3 22.5 - - - +
328B GLY* 4.0 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ARG* 2.8 28.8 + - + +
326A LEU* 4.0 17.5 - - + -
328A GLY* 1.3 72.3 - - - +
330A ALA* 1.3 63.8 + - - +
332A LEU* 3.1 23.9 + - - +
505A THR* 6.5 1.3 - - + -
325B ARG* 3.8 6.3 + - - +
329B ALA* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LEU* 2.7 26.8 + - + +
329A ALA* 1.3 74.0 - - - +
331A GLU* 1.4 54.8 + - - +
332A LEU* 2.9 8.0 + - - +
333A ALA* 3.2 18.2 + - - +
424A ALA* 3.8 20.1 - - + +
425A PHE* 4.2 9.0 - - + -
428A VAL* 3.5 24.0 - - + -
501A ILE* 5.8 0.3 - - - +
502A THR* 4.2 9.7 + - + +
505A THR* 6.3 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 3.3 20.1 - - + +
328A GLY* 3.1 16.6 + - - +
329A ALA 3.0 1.8 - - - -
330A ALA* 1.4 74.9 - - - +
332A LEU* 1.3 60.5 + - - +
333A ALA* 3.1 0.9 - - - -
334A GLN* 2.9 36.9 + - - +
421A GLN* 2.8 43.8 + - - +
425A PHE* 3.7 10.9 - - + -
321B SER* 2.6 49.1 + - - +
325B ARG* 3.8 8.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASP* 3.4 38.8 - - + +
114A SER* 3.5 36.1 - - - +
115A GLY* 5.4 2.9 - - - -
329A ALA 3.1 15.8 + - - +
330A ALA* 2.9 2.1 + - - +
331A GLU* 1.3 76.1 - - - +
333A ALA* 1.3 60.4 + - - +
334A GLN* 3.0 0.4 - - - -
335A ARG* 3.1 24.8 + - + +
336A SER* 4.5 0.7 + - - -
501A ILE* 5.3 1.3 - - + -
505A THR* 5.8 3.4 - - + +
316B VAL* 5.7 1.3 - - + +
325B ARG* 3.5 33.4 - - - +
509B GLU* 5.3 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ALA 3.2 13.1 + - - +
331A GLU* 3.0 0.6 + - - -
332A LEU* 1.3 75.5 - - - +
334A GLN* 1.4 61.9 + - - +
335A ARG 3.1 0.2 - - - -
336A SER* 3.0 17.9 + - - +
337A SER* 3.1 10.7 + - - -
420A THR* 3.9 19.0 - - + +
421A GLN* 5.6 1.1 - - - -
424A ALA* 4.5 12.6 - - + -
498A GLY* 4.6 1.3 - - - -
501A ILE* 3.9 39.9 - - + +
502A THR* 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLU* 2.9 28.9 + - - +
333A ALA* 1.4 77.7 - - - +
335A ARG* 1.4 57.3 + - - +
336A SER 3.2 0.2 - - - -
337A SER* 2.9 31.0 + - - -
338A TRP* 2.9 35.3 + - + +
417A GLY* 3.1 28.5 + - - +
420A THR* 4.6 2.1 - - - +
421A GLN* 3.1 34.2 - - - +
315B PHE* 3.7 21.9 - - + -
316B VAL* 3.8 13.8 - - + +
321B SER* 3.9 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ALA 3.1 30.9 + - - +
108A ALA* 3.5 13.6 - - - +
110A ALA* 3.3 32.8 - - - +
112A ASP* 2.8 39.8 + - - +
118A PHE* 4.3 8.1 - - + +
332A LEU* 3.1 23.0 + - + +
334A GLN* 1.4 79.2 - - - +
336A SER* 1.3 63.3 + - - +
338A TRP* 3.3 5.0 + - - +
339A TYR* 3.3 19.9 + - - +
316B VAL* 3.6 23.9 + - + +
317B ASN* 2.8 31.3 + - - -
325B ARG* 4.5 9.1 - - - +
513B PHE* 3.8 11.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PRO* 4.8 3.6 + - - +
117A ALA 4.1 3.6 + - - -
118A PHE* 3.6 33.2 + - - +
121A THR* 4.1 9.2 + - - -
332A LEU 4.5 0.5 + - - -
333A ALA* 3.0 4.5 + - - -
335A ARG* 1.3 74.8 - - - +
337A SER* 1.3 68.6 + - - +
339A TYR* 3.1 5.2 + - - +
340A GLN* 3.1 26.5 + - - +
497A LEU* 4.3 6.1 - - - -
501A ILE* 3.5 33.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ALA 3.1 12.1 + - - -
334A GLN* 2.9 31.8 + - - -
336A SER* 1.3 77.4 - - - +
338A TRP* 1.4 57.2 + - - -
340A GLN* 3.4 2.5 + - - +
341A LYS* 3.0 44.7 + - - +
415A PRO* 3.8 6.5 - - - +
417A GLY* 3.8 4.9 - - - -
420A THR* 3.8 19.6 + - - -
497A LEU* 4.0 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 2.9 29.3 + - + -
104A ASN* 3.1 21.8 + - + +
105A PRO* 4.7 0.4 - - + -
107A ALA* 3.7 10.8 - - + -
108A ALA* 4.4 9.6 - - + +
334A GLN* 2.9 43.5 + - + +
335A ARG* 3.6 6.5 - - - +
336A SER 3.2 0.4 - - - -
337A SER* 1.4 76.9 + - - +
339A TYR* 1.3 56.3 + - - +
341A LYS* 3.3 20.2 + - + -
342A TRP* 2.9 55.5 + + - +
343A GLN* 3.5 3.6 - - - +
411A HIS* 3.6 41.7 - + - -
417A GLY* 4.8 1.8 - - - -
315B PHE* 3.3 33.2 - + - -
316B VAL* 3.8 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 3.9 17.5 - - + -
108A ALA* 3.5 16.4 - - + +
109A PHE* 4.4 1.3 - + - -
118A PHE* 3.5 38.8 - + + +
119A SER* 3.5 22.8 - - - -
335A ARG 3.3 6.6 + - - +
336A SER 3.1 8.2 + - - +
338A TRP* 1.3 75.9 - - - +
340A GLN* 1.3 70.6 - - - +
343A GLN* 2.9 57.9 + - + +
344A VAL* 3.1 11.1 + - + +
9B ALA* 3.4 21.0 - - + +
11B ASP* 2.8 31.3 + - + -
18B ARG* 3.4 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 2.9 31.5 + - - +
118A PHE 4.9 2.0 + - - -
121A THR* 3.4 17.8 + - - -
122A THR* 4.0 1.4 - - - +
123A ILE* 3.6 24.5 + - + +
336A SER* 3.1 12.7 + - - +
337A SER 3.6 8.1 - - - +
339A TYR* 1.3 90.0 - - - +
341A LYS* 1.3 65.6 + - - +
344A VAL* 3.8 5.0 - - - +
345A HIS* 3.0 54.8 + - - +
414A TYR 3.7 2.7 - - - -
415A PRO* 3.6 15.3 - - + -
497A LEU* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A SER* 3.0 20.9 + - - +
338A TRP* 3.5 40.2 - - + +
340A GLN* 1.3 76.8 - - - +
342A TRP* 1.3 65.5 + - + +
346A ARG* 2.8 29.8 + - - -
349A ARG* 3.8 1.2 - - - +
411A HIS* 3.1 23.7 + - + +
412A PRO* 2.8 38.7 + - + +
414A TYR 3.2 18.3 + - - +
415A PRO 2.8 25.5 + - - +
417A GLY 3.9 2.0 - - - +
486A HIS* 4.0 1.2 - - - -
600A VO4 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PHE* 3.7 33.0 - + - -
74A LEU* 4.0 20.0 - - + -
78A ILE* 3.3 33.5 - - + +
102A LEU* 4.2 12.6 - - + -
103A VAL 3.6 14.1 + - - -
105A PRO* 3.8 25.1 - - + +
338A TRP* 2.9 62.6 + + - +
341A LYS* 1.3 79.8 - - + +
343A GLN* 1.3 75.2 + - - +
344A VAL 3.3 1.8 - - - -
346A ARG* 3.0 25.7 + - - +
410A THR 3.8 8.1 - - - -
411A HIS* 3.6 18.8 - - + +
412A PRO* 3.5 17.1 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il