Contacts of the strand formed by residues 306 - 310 (chain A) in PDB entry 3VG1
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 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A CYS* 3.2 0.9 - - - -
258A TRP 2.9 34.5 + - - +
259A GLN 4.8 0.2 - - - +
260A ALA* 3.3 11.4 - - - +
261A GLY* 2.7 31.4 + - - -
263A THR* 4.2 5.1 + - - +
305A ASP* 1.3 78.2 - - - +
307A CYS* 1.3 61.2 + - - +
308A TYR* 3.4 33.0 + - + +
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Residues in contact with CYS 307 (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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255A LEU* 4.3 7.9 - - + -
256A VAL 3.3 3.8 - - - +
257A CYS* 2.0 45.5 - - - -
296A PRO* 3.6 3.6 - - - +
297A VAL* 3.1 44.9 + - + +
302A THR* 3.7 30.1 - - - +
305A ASP* 3.7 6.5 + - - -
306A ASP* 1.3 73.8 - - - +
308A TYR* 1.3 68.4 + - - +
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Residues in contact with TYR 308 (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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249A PHE* 4.3 0.5 - - - -
255A LEU* 3.3 10.0 - - - -
256A VAL* 2.8 41.1 + - + +
258A TRP* 3.6 23.1 - + + -
263A THR* 2.8 30.8 + - + -
265A TRP* 3.4 28.8 - + - -
294A LEU* 3.5 32.3 - - + -
295A ARG 3.2 6.7 - - - +
296A PRO* 3.7 27.1 - - + -
297A VAL* 4.4 0.4 - - - -
306A ASP* 3.4 35.4 + - + +
307A CYS* 1.3 75.8 - - - +
309A LYS* 1.3 61.2 + - - +
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Residues in contact with LYS 309 (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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221A ASN* 6.3 0.9 - - - +
249A PHE* 4.4 2.7 - - - -
252A GLY* 2.9 32.5 + - - +
253A GLU 5.8 0.9 - - - -
254A GLN 5.0 2.2 - - - +
255A LEU* 3.4 22.9 - - + +
294A LEU* 3.6 3.4 - - - -
295A ARG* 2.9 69.4 + - + +
297A VAL* 4.1 4.7 - - + +
308A TYR* 1.3 74.8 - - - +
310A PHE* 1.3 72.4 + - - +
311A ALA* 3.2 1.3 + - - -
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Residues in contact with PHE 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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221A ASN* 4.2 5.7 + - - -
229A PHE* 4.4 0.2 - + - -
233A VAL* 4.1 15.3 - - + -
236A ILE* 4.1 10.5 - - + -
249A PHE* 3.4 42.2 + + + +
250A TRP* 3.7 53.6 - + - -
252A GLY* 4.4 8.4 - - - -
254A GLN 5.0 0.2 + - - -
293A TYR* 3.9 25.4 - + - -
294A LEU* 3.9 17.5 - - + -
309A LYS* 1.3 79.9 - - - +
311A ALA* 1.3 60.3 + - - +
312A ILE* 3.3 53.0 + - + +
313A SER* 5.7 0.2 - - - -
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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