Contacts of the strand formed by residues 289 - 294 (chain A) in PDB entry 3V4V
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 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A PHE* 3.4 5.5 - - - -
279A ALA* 3.4 5.5 - - - -
280A VAL 2.9 37.8 + - - +
281A ASP* 4.0 1.9 - - - +
282A LEU* 3.4 35.5 + - + +
283A ASN* 3.9 10.8 + - - +
285A ASP* 5.5 0.5 - - - +
287A PHE 5.5 0.8 - - - +
288A SER* 1.3 78.5 + - - +
290A LEU* 1.3 64.2 + - - +
309A TYR 3.6 5.2 - - - +
310A ILE* 2.8 27.7 - - - +
311A ASN* 2.3 37.9 + - - +
318A MET* 3.9 2.7 - - - -
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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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227A PHE* 4.1 3.8 - - + -
236A VAL* 3.8 31.6 - - + -
250A ILE* 3.6 37.0 - - + -
264A MET* 4.1 10.5 - - + -
277A VAL* 4.7 1.3 - - + -
278A CYS 3.4 10.3 - - - +
280A VAL* 4.5 0.4 - - - +
289A ASP* 1.3 80.7 - - - +
291A LEU* 1.3 95.3 + - - +
292A VAL* 3.4 23.3 - - + -
308A VAL* 4.5 0.3 - - - +
309A TYR* 2.9 38.9 + - + +
318A MET* 3.6 11.4 - - + -
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Residues in contact with LEU 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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276A SER 4.0 0.5 - - - +
277A VAL* 3.4 4.0 - - - -
278A CYS 2.8 38.2 + - - +
280A VAL* 4.3 11.9 - - + -
282A LEU* 4.3 9.6 - - + -
290A LEU* 1.3 90.2 - - - +
292A VAL* 1.3 60.4 + - - +
306A VAL* 4.3 10.8 - - + -
307A PHE 3.4 3.6 - - - +
308A VAL* 3.5 38.1 - - + -
325A LEU* 4.9 0.4 - - + -
339A ILE* 3.9 25.5 - - + +
353A VAL* 3.8 33.7 - - + -
355A ILE* 4.7 3.6 - - + -
377A ILE* 4.6 9.0 - - + -
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Residues in contact with VAL 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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248A ALA* 4.0 13.9 - - + -
264A MET* 5.0 1.3 - - - -
273A PHE* 3.5 37.0 - - + -
274A GLY* 3.3 34.5 - - - +
276A SER 3.6 4.0 - - - +
277A VAL* 4.4 4.7 - - + -
290A LEU* 3.4 23.8 - - + -
291A LEU* 1.3 73.1 - - - +
293A GLY* 1.3 63.5 + - - +
294A ALA 4.1 0.2 + - - -
306A VAL* 3.3 5.0 - - - +
307A PHE* 2.8 33.4 + - - -
309A TYR* 3.9 12.3 - - + -
339A ILE* 3.9 3.4 - - - -
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Residues in contact with GLY 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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272A TYR 3.5 0.3 - - - +
273A PHE* 5.3 0.4 - - - -
274A GLY 2.9 24.7 + - - -
275A ALA 3.3 9.1 + - - -
276A SER* 2.8 29.3 + - - -
292A VAL* 1.3 74.4 - - - +
294A ALA* 1.3 59.1 + - - -
295A PRO* 3.5 6.2 - - - +
305A ARG 3.7 4.7 - - - -
306A VAL* 4.2 2.7 - - - -
336A GLY 3.9 7.0 - - - -
339A ILE* 3.7 5.6 - - - +
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Residues in contact with ALA 294 (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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271A SER* 3.3 17.3 - - - +
272A TYR 3.9 1.1 - - - -
273A PHE* 3.7 15.9 - - + +
292A VAL 4.1 0.4 + - - -
293A GLY* 1.3 73.4 - - - +
295A PRO* 1.3 59.2 - - - +
296A MET 3.1 4.9 - - - -
297A GLN* 3.1 25.4 + - - +
305A ARG 2.7 25.6 + - - +
307A PHE* 3.8 25.1 - - + -
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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