Contacts of the helix formed by residues 326 - 345 (chain A) in PDB entry 1V8K
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 GLU 326 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A TYR* 3.7 24.2 + - - -
220A ASN* 3.5 37.0 + - - +
283A ARG* 4.0 29.6 + - - +
324A ARG* 2.8 24.4 + - + +
325A MET* 1.3 73.8 - - - +
327A GLY* 1.3 58.5 + - - +
328A ALA 2.8 6.3 - - - -
329A GLU* 2.9 25.0 + - + +
330A ILE* 3.1 21.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ARG 4.0 2.4 + - - -
325A MET* 3.1 2.6 - - - +
326A GLU* 1.3 82.3 - - - +
328A ALA* 1.3 56.6 + - - +
330A ILE* 3.7 14.9 - - - +
331A ASN* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A MET* 3.5 40.5 + - + +
327A GLY* 1.3 77.2 - - - +
329A GLU* 1.3 59.9 + - - +
331A ASN* 4.0 4.0 - - - +
332A LYS* 3.0 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ILE* 6.5 0.2 - - + -
220A ASN* 3.9 18.9 + - - +
221A GLY* 3.8 32.7 + - - +
285A HIS* 5.3 0.4 - - - -
326A GLU* 2.9 15.0 + - + +
328A ALA* 1.3 77.6 - - - +
330A ILE* 1.3 60.3 + - + +
332A LYS* 2.9 59.8 + - + +
333A SER* 3.0 14.9 + - - -
356A SER* 4.9 6.1 - - - -
357A LYS* 5.2 2.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A SER* 4.9 2.5 - - - +
283A ARG* 4.3 18.4 - - - +
285A HIS* 4.7 7.6 - - + +
308A ALA* 3.9 28.7 - - + +
309A GLY 3.6 23.1 - - - +
310A ASN* 5.1 1.8 - - - +
326A GLU* 3.1 20.5 + - + +
327A GLY* 3.7 14.8 - - - +
329A GLU* 1.3 80.2 - - + +
331A ASN* 1.3 57.7 + - - +
333A SER* 2.6 20.9 + - - +
334A LEU* 3.0 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ASN 5.3 6.1 + - - -
327A GLY 2.8 19.7 + - - +
328A ALA* 4.0 4.9 - - - +
330A ILE* 1.3 75.6 - - - +
332A LYS* 1.3 61.0 + - - +
334A LEU* 3.8 8.4 - - - +
335A LEU* 2.9 50.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ALA* 3.0 14.8 + - - +
329A GLU* 2.9 60.4 + - - +
331A ASN* 1.3 74.6 - - - +
333A SER* 1.3 55.7 + - - +
335A LEU* 3.3 11.7 + - - +
336A ALA* 2.7 35.2 + - - +
354A ARG* 4.4 7.2 - - + +
355A GLU 4.1 11.2 + - - +
356A SER* 4.0 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A HIS* 3.1 31.7 - - - -
329A GLU* 3.0 12.1 + - - -
330A ILE 2.6 23.4 + - - -
332A LYS* 1.3 81.1 - - - +
334A LEU* 1.3 51.8 + - - +
336A ALA* 3.5 1.4 - - - +
337A LEU* 2.6 36.8 + - - +
356A SER* 3.3 24.9 - - - -
358A LEU* 4.3 9.4 - - - +
359A THR* 4.2 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TYR* 3.8 25.4 - - + +
285A HIS* 4.7 5.2 - - + +
307A LEU* 4.1 25.4 - - + -
308A ALA 4.8 3.1 - - - +
310A ASN* 3.7 38.4 - - + +
330A ILE* 3.0 28.3 + - + +
331A ASN* 3.8 9.0 - - - +
332A LYS 3.3 0.2 - - - -
333A SER* 1.3 81.9 + - - +
335A LEU* 1.3 67.1 + - + +
337A LEU* 4.2 4.7 - - + -
338A LYS 3.1 9.0 + - - -
358A LEU* 5.5 0.2 - - + -
395A TYR* 3.0 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ASN* 2.9 45.5 + - - +
332A LYS* 3.6 8.5 - - - +
334A LEU* 1.3 78.5 - - + +
336A ALA* 1.3 62.9 + - - +
338A LYS* 3.5 24.2 + - - +
339A GLU* 3.3 27.6 + - - +
353A PHE 5.4 3.1 - - - +
395A TYR* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LYS 2.7 19.0 + - - +
333A SER 3.5 4.3 - - - +
335A LEU* 1.3 76.6 - - - +
337A LEU* 1.3 65.9 + - - +
339A GLU* 3.3 5.7 + - - +
340A CYS* 3.0 27.3 + - - -
353A PHE* 4.8 8.9 - - + +
354A ARG 3.8 19.5 - - - +
355A GLU* 4.6 1.8 - - - +
356A SER* 3.8 6.7 - - - +
359A THR* 3.6 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PHE* 3.5 42.2 - - + -
307A LEU* 3.8 33.9 - - + -
333A SER 2.6 21.3 + - - +
334A LEU* 3.6 8.7 - - + +
335A LEU 3.3 0.2 - - - -
336A ALA* 1.3 72.1 - - - +
338A LYS* 1.3 63.7 + - - +
340A CYS* 3.0 3.5 + - - +
341A ILE* 2.9 41.8 + - + +
358A LEU* 4.6 8.3 - - + -
359A THR* 3.5 13.4 - - + +
362A LEU* 5.5 0.2 - - + -
366A PHE* 4.0 12.6 - - + -
375A MET* 4.7 3.4 - - + -
395A TYR* 3.9 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LEU 3.1 12.6 + - - +
335A LEU* 3.7 23.0 - - - +
336A ALA 3.3 0.2 - - - -
337A LEU* 1.3 80.2 - - - +
339A GLU* 1.3 62.1 - - + +
341A ILE* 3.3 5.8 + - - +
342A ARG* 2.9 44.4 + - - +
395A TYR* 3.5 47.5 + - + +
398A ARG* 3.7 45.4 - - + +
399A VAL* 4.0 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU 3.3 14.3 + - - +
336A ALA* 3.3 8.1 + - - +
337A LEU 3.3 0.4 - - - -
338A LYS* 1.3 83.1 - - + +
340A CYS* 1.3 57.8 + - - +
342A ARG* 3.8 20.5 + - - +
343A ALA* 2.9 29.1 + - - +
353A PHE* 5.2 23.6 - - + +
398A ARG* 4.3 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ALA* 3.0 17.5 + - - +
337A LEU* 3.5 9.0 - - - +
339A GLU* 1.3 75.3 - - - +
341A ILE* 1.3 65.6 + - - +
343A ALA* 3.2 7.6 + - - +
344A LEU* 3.1 19.6 + - - +
353A PHE* 3.9 27.6 - - - -
355A GLU* 4.6 1.3 - - - -
359A THR* 3.7 26.5 - - - -
363A ARG* 6.3 0.2 - - - -
366A PHE* 3.8 39.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 4.2 13.9 - - + +
159A PHE* 4.0 14.8 - - + -
337A LEU* 2.9 46.5 + - + +
338A LYS* 3.7 4.5 - - - +
340A CYS* 1.3 73.0 - - - +
342A ARG* 1.3 62.4 + - - +
344A LEU* 3.0 27.8 + - - +
345A GLY 3.6 2.8 + - - -
366A PHE* 4.2 13.9 - - + -
373A THR* 3.9 22.9 - - + +
375A MET* 3.9 25.6 - - + -
399A VAL* 3.9 22.4 - - + +
402A LEU* 4.8 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LYS* 2.9 31.3 + - - +
339A GLU* 4.0 18.3 + - - +
341A ILE* 1.3 71.1 - - - +
343A ALA* 1.3 62.7 + - - +
344A LEU 3.0 4.9 - - - -
345A GLY 3.3 2.4 + - - -
346A GLN* 4.1 3.5 - - - +
398A ARG* 3.4 37.9 + - - +
399A VAL* 4.3 5.8 - - - +
401A GLU* 4.0 15.4 + - - -
402A LEU* 2.8 81.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLU 2.9 20.5 + - - +
340A CYS* 3.5 9.6 - - - +
341A ILE 3.2 0.2 - - - -
342A ARG* 1.3 76.5 - - - +
344A LEU* 1.3 60.3 + - - +
345A GLY 3.4 0.2 - - - -
346A GLN* 3.1 23.4 + - - +
353A PHE* 5.4 10.5 - - + -
366A PHE 5.0 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 3.3 39.2 + - + +
73A ILE* 5.3 0.9 - - + -
340A CYS 3.1 7.9 + - - +
341A ILE* 3.0 18.1 + - - +
343A ALA* 1.3 81.0 - - - +
345A GLY* 1.3 55.8 + - - +
346A GLN 3.1 7.6 + - - +
365A SER 5.1 0.9 - - - +
366A PHE* 3.7 28.7 - - + +
368A GLY 4.2 4.9 - - - +
369A GLU* 5.9 0.9 - - - +
371A SER* 3.1 39.5 - - - +
372A ARG 4.4 0.7 - - - -
373A THR* 3.6 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 3.6 21.8 - - - -
73A ILE* 5.3 2.2 - - - +
341A ILE 3.6 1.8 + - - -
342A ARG 3.3 4.9 + - - -
344A LEU* 1.3 78.2 - - - +
346A GLN* 1.3 60.6 + - - +
402A LEU* 2.7 36.9 - - - +
----------------------------------------------------------
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