Contacts of the helix formed by residues 319 - 339 (chain A) in PDB entry 1ZY7
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 LEU 319 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A HIS* 1.3 71.0 - - - +
320A PRO* 1.3 69.8 - - + +
321A GLN 3.4 0.9 - - - +
322A VAL* 3.3 30.9 + - + +
323A LEU* 2.9 27.7 + - - +
680B ILE* 4.4 13.6 - - + +
683B GLY* 6.3 0.9 - - - -
685B GLY* 3.9 30.5 - - - +
686B ALA* 4.2 15.7 - - + +
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Residues in contact with PRO 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A PRO* 4.2 18.6 - - + -
311A PRO* 6.1 0.2 - - + -
316A GLN* 3.2 25.6 - - - +
318A HIS 3.2 8.0 - - - +
319A LEU* 1.3 87.4 - - + +
321A GLN* 1.3 58.3 + - - +
323A LEU* 3.3 2.5 + - + +
324A ALA* 2.8 30.2 + - - +
580A LEU* 3.8 34.0 - - + +
582A SER* 4.4 2.0 + - - +
680B ILE* 4.1 8.7 - - + +
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Residues in contact with GLN 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ARG 5.5 1.6 - - - +
309A PRO* 4.0 16.3 - - + +
319A LEU* 3.4 0.8 - - - +
320A PRO* 1.3 79.4 - - - +
322A VAL* 1.3 59.0 + - + +
324A ALA* 3.4 2.2 + - - +
325A ASP* 3.0 60.6 + - - +
582A SER* 3.6 11.6 + - - -
583A GLY 3.0 25.7 + - - +
584A ILE* 3.6 6.5 - - - +
585A SER* 3.7 18.4 - - - +
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A HIS* 6.3 0.7 - - + -
319A LEU* 3.3 39.9 + - + +
321A GLN* 1.3 76.4 - - + +
323A LEU* 1.3 59.0 - - - +
325A ASP* 3.5 4.5 + - - +
326A ALA* 3.0 29.3 + - + +
363A VAL* 4.5 22.7 - - + -
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A GLN* 6.5 0.7 - - + -
318A HIS* 3.9 27.3 - - + +
319A LEU 2.9 20.5 + - - +
320A PRO 3.6 3.6 - - - +
322A VAL* 1.3 72.6 - - - +
324A ALA* 1.3 58.9 + - - +
326A ALA* 3.3 3.7 + - - +
327A VAL* 2.8 53.2 + - + +
358A THR* 4.3 7.4 - - + -
363A VAL* 4.2 19.1 - - + -
443A HIS* 3.7 24.0 - - + +
544A SER* 3.4 27.6 - - - +
546A ILE* 5.4 1.1 - - + -
580A LEU* 4.1 12.8 - - + -
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PRO 2.8 18.7 + - - +
321A GLN* 3.6 7.0 - - - +
322A VAL 3.3 0.2 - - - -
323A LEU* 1.3 77.6 - - - +
325A ASP* 1.3 59.2 + - - +
327A VAL 3.5 0.2 + - - -
328A SER* 2.9 29.0 + - - -
546A ILE* 3.6 31.2 - - + +
582A SER* 3.6 9.4 - - - +
583A GLY 3.4 25.8 - - - +
584A ILE* 4.3 0.7 - - - -
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Residues in contact with ASP 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A GLN* 3.0 29.4 + - - +
322A VAL* 4.0 4.3 - - - +
324A ALA* 1.3 73.4 - - - +
326A ALA* 1.3 60.1 + - - +
328A SER* 3.0 6.0 + - - -
329A ARG* 2.9 32.7 + - - +
584A ILE* 3.5 4.3 - - - +
585A SER* 2.6 50.2 + - - -
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 3.0 19.5 + - + +
323A LEU 3.7 3.1 - - - +
325A ASP* 1.3 74.9 - - - +
327A VAL* 1.3 68.2 + - + +
329A ARG* 3.3 24.3 + - - +
330A LEU* 2.9 35.5 + - + +
363A VAL* 3.9 26.5 - - + +
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Residues in contact with VAL 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 2.8 49.8 + - + +
324A ALA 4.5 0.2 - - - +
326A ALA* 1.3 72.8 - - + +
328A SER* 1.3 59.9 + - - +
330A LEU* 3.3 3.7 + - + +
331A VAL* 2.9 34.0 + - - +
356A VAL* 3.8 30.1 - - + -
443A HIS* 4.1 20.6 - - + +
445A TYR* 3.7 26.5 - - + +
546A ILE* 4.1 19.3 - - + -
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Residues in contact with SER 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ALA 2.9 19.4 + - - -
325A ASP* 3.0 16.8 + - - -
327A VAL* 1.3 78.9 - - - +
329A ARG* 1.3 60.3 + - - +
331A VAL* 3.5 1.2 + - - +
332A LEU* 3.1 25.3 + - - +
445A TYR* 3.4 41.8 - - - -
584A ILE* 3.5 20.1 - - - +
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Residues in contact with ARG 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ASP 2.9 16.5 + - - +
326A ALA* 3.7 26.4 - - - +
328A SER* 1.3 78.8 + - - +
330A LEU* 1.3 87.1 + - - +
332A LEU* 3.8 6.7 - - - +
333A GLY* 2.9 27.0 + - - -
363A VAL* 5.7 4.4 + - - +
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ALA* 2.9 31.6 + - + +
327A VAL* 3.7 3.8 - - + +
329A ARG* 1.3 100.7 - - - +
331A VAL* 1.3 63.7 + - - +
333A GLY* 3.3 1.4 + - - -
334A LYS* 3.0 25.6 + - - +
356A VAL* 4.2 11.9 - - + -
363A VAL 5.3 0.9 - - - +
366A ALA* 3.7 37.7 - - + +
368A VAL* 3.6 20.9 - - + +
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A VAL 2.9 19.8 + - - +
328A SER 4.1 0.4 - - - +
330A LEU* 1.3 76.6 - - - +
332A LEU* 1.3 63.7 + - - +
334A LYS* 3.3 3.1 + - - +
335A PHE* 2.9 22.5 + - - +
352A LEU* 4.1 11.7 - - + -
353A ALA 3.6 27.1 - - - +
354A GLY* 3.9 20.0 - - - +
355A VAL 4.5 0.4 - - - +
356A VAL* 3.7 20.4 - - + -
368A VAL* 4.6 8.3 - - + -
371A VAL* 4.0 11.2 - - + +
445A TYR* 4.0 25.4 - - + -
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Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A SER 3.1 17.9 + - - +
329A ARG* 3.8 5.4 - - - +
331A VAL* 1.3 77.7 - - - +
333A GLY* 1.3 56.2 + - - +
335A PHE* 3.3 5.0 + - + +
336A GLY 2.9 24.1 + - - -
342A PHE* 3.3 36.8 - - + -
349A ARG* 4.2 16.6 - - - +
352A LEU* 3.8 25.9 - - + +
445A TYR* 6.1 0.4 - - + -
588A GLU* 5.0 4.9 - - - +
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Residues in contact with GLY 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ARG 2.9 17.6 + - - -
330A LEU* 3.8 1.8 - - - -
331A VAL 3.3 0.2 - - - -
332A LEU* 1.3 74.4 - - - +
334A LYS* 1.3 58.4 + - - +
336A GLY* 3.1 2.8 + - - -
337A ASP* 2.9 36.3 + - - +
342A PHE* 5.0 3.6 - - - -
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Residues in contact with LYS 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A LEU 3.0 17.0 + - - +
331A VAL 3.7 3.4 - - - +
333A GLY* 1.3 74.1 - - - +
335A PHE* 1.3 65.3 + - - +
337A ASP* 3.2 20.2 + - + +
338A LEU* 2.9 38.4 + - + +
368A VAL* 4.0 17.3 - - + -
371A VAL* 3.7 13.5 - - + -
602A TRP* 3.7 44.9 - - + -
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Residues in contact with PHE 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A VAL 2.9 13.4 + - - +
332A LEU* 3.4 9.2 - - + +
334A LYS* 1.3 76.2 - - - +
336A GLY* 1.3 59.3 + - - +
338A LEU* 3.3 4.6 + - + +
339A THR* 2.8 45.3 + - + +
342A PHE* 3.9 22.4 - + - -
346A HIS 4.0 3.4 - - - -
347A ALA* 3.6 39.0 - - - -
349A ARG* 4.0 13.0 - - + -
352A LEU* 3.6 21.3 - - + -
371A VAL* 3.5 27.5 - - + +
373A THR* 3.5 28.7 - - + -
600A VAL* 4.2 14.1 - - + -
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Residues in contact with GLY 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A LEU 2.9 11.7 + - - -
333A GLY 3.1 2.6 + - - -
335A PHE* 1.3 77.0 - - - +
337A ASP* 1.3 60.0 + - - +
339A THR* 3.1 12.1 + - - -
341A ASN* 2.7 32.2 + - - -
342A PHE* 3.2 35.6 - - - -
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Residues in contact with ASP 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A GLY 2.9 20.2 + - - +
334A LYS* 3.2 27.4 + - + +
336A GLY* 1.3 76.9 - - - +
338A LEU* 1.3 62.5 + - + +
340A ASP* 3.5 9.2 + - - -
341A ASN* 4.3 12.9 + - - +
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Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LYS* 2.9 36.6 + - + +
335A PHE* 3.7 7.0 - - + +
337A ASP* 1.3 76.7 - - + +
339A THR* 1.3 61.6 + - + +
340A ASP 3.4 1.7 + - - -
344A SER* 5.4 0.2 - - - -
371A VAL* 4.3 9.9 - - + -
602A TRP* 3.5 61.9 - - + +
607A SER 4.9 4.5 - - - +
608A ALA* 4.8 5.8 - - - -
609A ILE* 3.7 36.1 + - + +
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Residues in contact with THR 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A PHE* 2.8 49.9 + - + +
336A GLY* 3.1 2.6 + - - -
338A LEU* 1.3 82.8 - - + +
340A ASP* 1.3 62.0 + - - +
342A PHE* 3.2 20.4 + - - -
343A SER 2.9 22.5 + - - -
344A SER* 2.9 21.2 + - - -
346A HIS 4.4 3.4 - - - +
347A ALA* 3.8 23.1 - - - +
609A ILE* 4.8 9.6 - - + -
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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) + - + + + + + -
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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