Contacts of the helix formed by residues 277 - 282 (chain B) in PDB entry 6G4N
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 VAL 277 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B LEU* 3.8 19.5 - - + -
251B ASN* 4.2 26.5 - - + +
252B LEU* 3.7 27.1 - - + -
273B GLU 3.4 17.9 - - - +
274B LEU 3.5 4.9 - - - +
276B ASP* 1.3 82.2 - - + +
278B GLU* 1.3 70.1 + - - +
279B TRP 3.1 2.9 - - - -
280B ASN* 2.7 32.0 + - - +
281B VAL* 4.4 3.1 - - - +
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Residues in contact with GLU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B TYR* 4.9 8.0 + - - +
121B TYR* 3.3 31.7 - - - +
151B GLY* 4.4 14.8 - - - -
152B ALA* 4.5 4.3 + - + +
248B LEU* 4.7 3.1 - - - -
274B LEU 2.9 14.2 + - - +
275B ILE* 3.1 36.6 + - + +
277B VAL* 1.3 75.0 - - - +
279B TRP* 1.3 83.6 + - + +
280B ASN 3.3 0.7 + - - -
281B VAL* 3.7 12.0 - - - +
291B SER* 2.9 35.1 + - - +
292B PHE* 4.2 14.2 + - + -
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Residues in contact with TRP 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B TYR* 3.5 26.7 - + - +
121B TYR* 3.9 44.6 - + - -
275B ILE 4.8 3.1 - - - -
276B ASP 6.0 1.1 - - - -
277B VAL 2.8 4.0 + - - -
278B GLU* 1.3 87.9 - - + +
280B ASN* 1.3 53.6 + - - +
281B VAL 2.7 17.3 + - - -
282B LEU* 3.4 33.4 + - + +
289B ARG 3.6 21.1 - - - -
290B PHE* 4.3 10.1 - + + -
291B SER* 3.7 9.0 - - - -
603B E2W 3.3 100.0 - + + +
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Residues in contact with ASN 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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247B GLU* 4.5 8.8 - - - +
251B ASN* 3.1 32.3 + - - +
276B ASP 5.0 2.4 + - - +
277B VAL* 2.7 34.7 + - - +
279B TRP* 1.3 68.7 - - - +
281B VAL* 1.3 59.1 + - + +
282B LEU 3.7 3.4 - - - +
603B E2W 3.7 28.0 - - - +
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ARG* 3.1 19.4 + - - -
244B ARG* 3.3 46.9 - - + +
247B GLU* 4.1 15.0 - - + +
248B LEU* 3.9 32.3 - - + +
251B ASN* 5.0 2.2 - - - +
277B VAL 4.4 5.4 - - - +
278B GLU 3.7 17.7 - - - +
279B TRP 2.7 9.5 + - - -
280B ASN* 1.3 78.1 - - + +
282B LEU* 1.3 65.5 + - - +
291B SER* 4.4 4.9 - - - +
292B PHE* 4.7 4.7 - - + -
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Residues in contact with LEU 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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243B ARG* 4.7 1.6 + - - +
244B ARG* 4.2 14.6 - - - +
279B TRP* 3.4 38.3 + - + +
280B ASN 3.7 3.5 - - - +
281B VAL* 1.3 82.8 + - - +
283B PRO* 1.3 71.5 - - + +
284B PHE 3.4 11.7 + - - +
286B SER* 4.5 10.8 - - - +
289B ARG* 3.7 15.9 - - + +
290B PHE 3.5 37.7 - - - +
291B SER* 3.7 13.2 + - - +
603B E2W 4.8 8.7 - - + +
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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