Contacts of the strand formed by residues 285 - 293 (chain A) in PDB entry 3VAG
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 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A LYS* 4.4 10.8 - - + -
279A LEU* 4.1 19.3 - - + -
280A THR* 3.8 28.2 - - + +
284A PRO* 1.3 76.7 - - - +
286A LYS* 1.3 59.5 + - - +
287A ALA 3.9 8.1 - - - +
288A PHE* 4.3 20.6 - - + -
305A CYS* 3.9 17.0 - - + -
306A GLU 3.5 12.6 - - - +
307A TYR* 3.5 37.7 - - + +
308A VAL* 3.9 6.4 - - - +
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Residues in contact with LYS 286 (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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233A GLN* 3.8 20.4 + - - +
234A PRO* 4.4 22.4 + - - +
235A LEU 5.3 1.4 + - - -
236A PRO* 5.6 4.4 - - - +
285A LEU* 1.3 73.3 - - - +
287A ALA* 1.3 61.5 + - + +
306A GLU* 2.9 46.3 + - + +
307A TYR 3.6 20.9 - - - +
308A VAL* 3.9 21.1 + - + +
310A ILE* 5.5 0.9 - - - -
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Residues in contact with ALA 287 (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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285A LEU* 3.6 6.3 - - - +
286A LYS* 1.3 80.3 - - + +
288A PHE* 1.3 64.9 + - - +
305A CYS* 3.4 5.0 - - - +
306A GLU* 3.2 39.7 + - + +
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Residues in contact with PHE 288 (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 ASP* 3.9 21.1 - - + -
275A VAL* 3.9 20.2 - - + -
276A LYS* 3.6 39.7 - - + +
279A LEU* 3.6 31.4 - - + -
285A LEU* 4.3 10.5 - - + -
287A ALA* 1.3 78.2 - - - +
289A ASN* 1.3 66.3 + - - +
290A LEU* 3.9 28.5 - - + -
303A ALA* 4.0 15.7 - - + -
304A PHE 3.4 15.3 - - - -
305A CYS* 4.0 2.9 - - + -
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Residues in contact with ASN 289 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A LYS* 5.2 4.9 + - - -
272A ASP* 5.7 0.4 - - - -
288A PHE* 1.3 84.1 - - - +
290A LEU* 1.3 62.3 + - - +
291A VAL* 3.8 19.0 + - - +
303A ALA* 3.3 3.3 - - - -
304A PHE* 3.0 57.1 + - - +
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Residues in contact with LEU 290 (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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266A LEU* 4.3 6.1 - - + -
270A LEU 3.8 11.9 - - - +
271A ASN* 3.8 9.4 - - - +
272A ASP* 3.1 47.4 + - - +
275A VAL* 4.3 15.9 - - + -
288A PHE* 3.9 12.8 - - + -
289A ASN* 1.3 73.3 - - - +
291A VAL* 1.3 62.5 + - - +
292A LYS* 3.0 26.3 + - + +
299A SER* 3.8 24.7 - - - +
301A GLY* 5.4 0.2 - - - -
302A TYR 3.6 20.0 - - - +
303A ALA* 4.0 11.0 - - + -
401A DIO 4.9 0.4 - - - -
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Residues in contact with VAL 291 (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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289A ASN* 4.1 11.7 - - - +
290A LEU* 1.3 71.4 - - - +
292A LYS* 1.3 66.5 + - - +
299A SER* 3.7 2.9 + - - -
300A LYS* 2.9 36.7 + - + +
302A TYR* 3.1 56.7 + - + +
304A PHE* 3.9 24.2 - - + -
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Residues in contact with LYS 292 (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 ASP* 2.8 39.4 + - - +
290A LEU* 3.0 25.1 + - + +
291A VAL* 1.3 82.3 - - - +
293A ASP* 1.3 64.9 + - - +
294A SER* 3.4 5.7 + - - -
297A GLY* 3.6 24.2 - - - +
298A LEU 3.3 9.0 - - - +
299A SER* 4.0 11.4 - - - +
300A LYS* 4.0 11.0 - - - -
401A DIO 4.0 13.2 - - - -
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Residues in contact with ASP 293 (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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292A LYS* 1.3 69.0 - - - +
294A SER* 1.3 55.8 + - - +
295A ALA* 3.3 12.9 + - - +
296A THR* 2.9 44.7 + - - +
297A GLY* 2.5 37.3 + - - -
298A LEU* 2.8 15.7 + - + +
300A LYS* 4.0 22.5 + - + +
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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