Contacts of the strand formed by residues 279 - 285 (chain B) in PDB entry 3V9G
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 279 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203B PHE* 3.6 30.1 - - + +
205B ALA* 4.3 5.8 - - + -
273B VAL* 3.5 28.9 - - + +
274B THR* 4.1 7.0 - - - -
276B SER 3.3 9.1 + - - +
277B GLU 3.5 0.9 - - - +
278B HIS* 1.3 77.9 - - - +
280B CYS* 1.3 59.8 + - - +
281B GLY 3.4 25.6 - - - +
282B ILE* 4.0 16.6 - - + -
298B VAL* 3.8 29.4 - - + -
305B PHE* 4.0 15.2 - - + +
307B THR* 4.4 7.8 + - - +
309B PRO* 3.7 19.3 - - + +
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Residues in contact with CYS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B LEU* 3.4 40.4 - - + +
201B GLU 3.3 19.7 - - - +
202B GLY* 3.5 22.7 - - - -
203B PHE 3.0 23.0 + - - -
204B VAL* 4.0 7.4 - - - -
228B ASN* 4.5 0.7 - - - -
278B HIS 3.3 0.2 + - - -
279B LEU* 1.3 74.4 - - - +
281B GLY* 1.3 59.2 + - - +
307B THR* 4.2 11.4 - - + -
308B PHE 4.2 2.1 - - - +
309B PRO* 3.4 10.8 - - - +
310B ARG* 3.0 17.3 + - - +
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Residues in contact with GLY 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B PHE 3.7 3.8 + - - -
204B VAL* 3.4 13.2 - - - -
205B ALA 2.9 24.9 + - - -
279B LEU* 3.4 12.4 - - - +
280B CYS* 1.3 83.5 - - - +
282B ILE* 1.3 63.4 + - - -
309B PRO* 4.6 2.0 - - - -
310B ARG 3.1 13.9 - - - -
541B TRP* 4.4 5.4 - - - -
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Residues in contact with ILE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B ALA* 3.4 13.5 - - + +
207B ILE* 4.2 16.4 - - + -
273B VAL* 5.0 4.3 - - + -
274B THR* 4.0 26.7 - - + -
279B LEU* 4.0 14.4 - - + -
281B GLY* 1.3 79.2 - - - +
283B ASN* 1.3 61.8 + - - +
284B PHE* 4.2 18.8 - - + -
291B PHE* 5.6 2.0 - - + -
294B LEU* 4.4 20.2 - - + -
298B VAL* 4.1 15.0 - - + -
310B ARG 2.8 9.6 + - - +
311B LEU* 3.5 18.3 - - + +
312B ALA 2.9 29.8 + - - +
541B TRP* 4.0 3.9 - - - -
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Residues in contact with ASN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B VAL* 4.4 5.4 - - + +
205B ALA 2.9 12.3 + - - +
206B ALA* 3.5 2.6 - - - -
207B ILE 3.0 25.6 + - - +
219B LEU* 2.8 48.1 + - - +
223B PRO* 3.7 6.5 - - - +
281B GLY 4.2 0.6 - - - -
282B ILE* 1.3 71.2 - - - +
284B PHE* 1.3 60.8 + - - +
312B ALA* 3.7 11.1 - - - +
537B TYR* 3.0 28.3 + - - -
541B TRP* 3.3 28.5 - - + -
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Residues in contact with PHE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ILE* 3.8 27.4 - - + -
219B LEU* 4.4 1.7 - - - +
282B ILE* 4.2 11.4 - - + -
283B ASN* 1.3 74.9 + - - +
285B THR* 1.3 72.1 + - - +
286B GLY* 3.4 20.9 - - - -
287B SER 3.4 36.3 - - - -
290B THR* 3.8 27.8 - - + -
291B PHE* 3.6 33.4 - + + -
294B LEU* 3.9 13.7 - - + -
312B ALA 2.9 14.2 + - - +
313B GLY* 3.3 4.2 - - - -
314B GLU* 2.9 25.9 + - - +
315B CYS* 4.4 2.0 - - - -
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Residues in contact with THR 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ILE* 3.2 16.0 + - - +
208B SER 4.2 1.0 - - - -
209B PRO* 3.6 40.9 - - + +
215B ILE* 3.8 18.9 - - + +
219B LEU* 3.5 19.9 - - - +
284B PHE* 1.3 87.1 + - - +
286B GLY* 1.3 61.4 + - - +
314B GLU* 3.3 28.0 - - + +
348B CYS* 5.0 12.8 - - - -
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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