Contacts of the helix formed by residues 319 - 329 (chain A) in PDB entry 1VJZ
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 ASP 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A HIS* 2.7 38.1 + - - -
299A GLY 5.1 0.2 - - - +
300A ILE* 2.8 24.2 + - - +
303A SER* 4.6 3.2 + - - +
305A ARG* 4.2 6.9 + - - -
308A VAL* 4.0 12.6 - - - +
309A GLU 5.8 0.2 - - - -
310A TYR* 3.8 16.0 - - + -
318A LEU* 1.3 70.6 - - - +
320A ARG* 1.3 63.0 + - - +
321A LYS* 3.6 3.8 + - - +
322A MSE 3.2 35.9 + - + +
323A LEU* 3.0 22.0 + - - +
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Residues in contact with ARG 320 (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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36A TRP* 4.2 4.2 - - - +
311A GLU* 2.9 50.2 + - + +
313A TRP* 3.8 15.6 - - - -
318A LEU* 3.2 21.9 + - - +
319A ASP* 1.3 72.8 + - - +
321A LYS* 1.3 59.0 + - + +
323A LEU* 3.6 16.2 - - - +
324A GLU* 2.8 73.4 + - + +
327A ARG* 3.6 13.1 - - - +
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Residues in contact with LYS 321 (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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268A HIS* 4.2 14.8 - - + -
272A LEU* 4.0 24.3 - - + +
319A ASP* 3.2 7.7 + - - +
320A ARG* 1.3 79.7 - - + +
322A MSE 1.3 61.8 + - - +
324A GLU* 3.5 4.5 + - - +
325A LEU* 3.0 23.7 + - - +
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Residues in contact with MSE 322 (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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262A ALA 5.6 1.1 - - - +
268A HIS* 4.6 1.1 - - - +
271A VAL* 3.6 31.2 - - + -
272A LEU* 3.9 16.1 - - + +
275A LEU* 3.9 21.5 - - + -
291A LEU* 4.2 10.8 - - - -
298A PHE 4.7 3.6 - - - +
299A GLY 3.6 23.6 - - - +
300A ILE* 3.8 15.9 - - + -
305A ARG* 4.1 19.5 - - - +
319A ASP* 3.2 34.7 + - + +
321A LYS* 1.3 78.0 - - - +
323A LEU* 1.3 64.4 + - - +
325A LEU* 3.4 3.5 + - - +
326A LEU* 3.1 24.1 + - + +
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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
----------------------------------------------------------
36A TRP* 3.5 44.4 - - + +
38A PHE* 3.8 14.4 - - + -
300A ILE* 3.6 29.5 - - + +
318A LEU* 3.9 17.9 - - + -
319A ASP 3.0 16.9 + - - +
320A ARG* 3.6 26.0 - - - +
322A MSE 1.3 75.8 - - - +
324A GLU* 1.3 66.0 + - - +
326A LEU* 3.0 6.5 + - - +
327A ARG* 2.9 42.1 + - - +
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Residues in contact with GLU 324 (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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320A ARG* 2.8 66.2 + - + +
321A LYS* 4.1 5.2 - - - +
323A LEU* 1.3 74.0 - - - +
325A LEU* 1.3 62.6 + - - +
327A ARG* 3.0 32.2 + - - +
328A LYS* 3.0 24.3 + - - +
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Residues in contact with LEU 325 (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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272A LEU* 3.6 45.3 - - + +
275A LEU* 4.0 19.7 - - + -
276A GLU* 3.7 30.7 - - + +
279A LEU* 3.8 10.0 - - + +
321A LYS 3.0 13.4 + - - +
322A MSE 3.5 8.5 - - - +
323A LEU 3.2 0.2 - - - -
324A GLU* 1.3 76.3 - - - +
326A LEU* 1.3 61.2 + - + +
328A LYS* 3.3 11.3 + - + +
329A TYR* 3.3 42.9 - - + -
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Residues in contact with LEU 326 (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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9A ARG* 2.9 18.8 + - - -
11A PHE* 4.4 11.4 - - + -
38A PHE* 3.8 15.7 - - + -
260A MSE 3.7 29.4 - - + -
275A LEU* 4.5 7.0 - - + -
279A LEU* 3.8 21.8 - - + -
289A PHE* 4.0 11.1 - - + -
291A LEU* 3.9 17.0 - - + -
300A ILE* 3.7 25.4 - - + -
322A MSE 3.1 18.4 + - + +
323A LEU* 3.0 8.8 + - - +
325A LEU* 1.3 76.4 - - - +
327A ARG* 1.3 61.4 - - - +
329A TYR* 3.1 13.3 + - - +
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Residues in contact with ARG 327 (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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9A ARG* 3.7 9.5 + - - +
35A GLN 4.2 3.8 + - - -
36A TRP* 3.5 42.8 + - - +
37A ASP* 3.8 17.8 + - - -
38A PHE* 4.0 10.3 - - + -
320A ARG* 3.6 12.7 - - - +
323A LEU* 2.9 31.3 + - + +
324A GLU* 3.0 41.3 + - - +
326A LEU* 1.3 77.3 - - - +
328A LYS* 1.3 62.3 + - - +
329A TYR* 3.3 4.9 + - - +
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Residues in contact with LYS 328 (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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276A GLU* 3.2 17.4 + - - +
283A LYS* 4.4 10.2 + - - -
324A GLU 3.0 13.7 + - - +
325A LEU* 3.4 15.7 - - + +
326A LEU 3.2 0.2 - - - -
327A ARG* 1.3 78.3 - - - +
329A TYR* 1.3 91.9 + - + +
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Residues in contact with TYR 329 (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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7A ARG* 2.8 30.5 + - - -
9A ARG* 2.9 32.0 + - - -
276A GLU* 2.6 46.6 + - + +
279A LEU* 3.9 37.3 - - + +
280A GLU* 3.6 29.8 - - + +
283A LYS* 3.8 31.1 - - + +
289A PHE* 3.6 12.2 - - - -
325A LEU* 3.3 29.4 - - + +
326A LEU 3.1 8.4 + - - +
327A ARG 3.8 1.9 - - - +
328A LYS* 1.3 105.3 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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