Contacts of the strand formed by residues 309 - 314 (chain A) in PDB entry 2VGB
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 LYS 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A ASP 3.3 8.3 + - - +
282A ILE* 3.2 7.7 - - + +
283A VAL 2.9 24.9 + - - -
307A GLY 3.4 7.4 + - - +
308A ILE* 1.3 72.6 - - - +
310A ILE* 1.3 60.7 + - - +
311A ILE* 4.0 0.9 - - + -
331A ASP* 3.3 27.4 + - + +
477A THR 5.2 10.4 + - - -
482A GLN* 5.0 9.3 + - - -
505A GLN* 3.6 39.3 - - + +
508A LEU* 4.0 23.8 - - + -
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Residues in contact with ILE 310 (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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283A VAL* 3.8 8.3 - - + +
285A ALA* 4.8 6.3 - - + -
294A VAL* 4.3 22.4 - - + +
297A VAL* 3.3 37.0 - - + -
298A ARG* 4.2 31.9 - - - +
301A LEU* 3.9 18.2 - - + -
308A ILE 3.9 10.3 - - - +
309A LYS* 1.3 76.0 - - - +
311A ILE* 1.3 69.6 + - - +
312A SER* 4.0 5.8 + - - +
330A SER* 4.1 1.5 - - - -
331A ASP* 2.7 44.6 + - - +
332A GLY 3.4 1.0 + - - -
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Residues in contact with ILE 311 (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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282A ILE* 3.7 24.0 - - + -
283A VAL 2.8 9.3 + - - -
284A PHE* 3.5 27.1 - - + -
285A ALA 2.8 26.4 + - - -
310A ILE* 1.3 78.9 - - - +
312A SER* 1.3 59.1 + - - +
313A LYS 3.4 0.5 + - - -
331A ASP* 4.3 4.9 - - + +
332A GLY* 3.7 23.6 - - - +
333A ILE 3.6 31.0 - - - +
334A MET* 3.6 9.9 - - + +
366A PRO* 4.8 3.1 - - + -
368A VAL* 4.6 5.2 - - + -
508A LEU* 4.0 29.6 - - + -
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Residues in contact with SER 312 (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 ALA* 4.0 1.8 - - - -
288A VAL* 3.6 27.4 - - - +
294A VAL* 4.2 8.0 - - - +
310A ILE* 4.0 3.2 - - - +
311A ILE* 1.3 70.9 - - - +
313A LYS* 1.3 62.1 + - - +
314A ILE* 3.7 1.0 + - - -
326A ILE* 3.7 23.0 - - - +
330A SER* 2.6 26.5 + - - -
332A GLY 3.1 7.1 + - - -
333A ILE* 3.3 13.8 - - - +
334A MET 2.9 19.7 + - - -
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Residues in contact with LYS 313 (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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116A ARG* 4.0 0.2 - - - +
156A ASP* 2.7 29.1 + - - +
284A PHE* 3.9 7.0 - - + -
285A ALA 3.0 24.2 + - - +
286A SER* 2.6 32.5 + - - +
287A PHE 4.1 1.2 + - - -
288A VAL* 3.3 29.3 + - - +
311A ILE 4.2 0.9 - - - +
312A SER* 1.3 72.4 - - - +
314A ILE* 1.3 61.5 + - - +
315A GLU* 3.7 13.8 + - + -
334A MET* 3.5 44.0 - - + -
336A ALA* 4.1 8.1 - - + -
581A PGA 3.6 27.2 + - - -
582A K 3.7 0.6 - - - -
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Residues in contact with ILE 314 (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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288A VAL 3.9 18.2 - - - +
312A SER* 4.7 1.3 - - - +
313A LYS* 1.3 72.3 - - - +
315A GLU* 1.3 61.3 + - - +
316A ASN 4.5 0.4 - - - +
319A GLY 3.9 14.4 - - - +
320A VAL* 3.8 32.8 - - + +
323A PHE* 4.3 4.7 - - + -
326A ILE* 4.0 25.1 - - + -
333A ILE* 4.0 22.9 - - + -
334A MET 2.9 11.9 + - - +
336A ALA* 3.2 23.2 + - - +
340A LEU* 4.1 7.4 - - + +
356A MET* 3.6 34.5 - - + -
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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