Contacts of the helix formed by residues 382 - 387 (chain B) in PDB entry 4GID
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 GLY 382 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B ASP 3.3 11.0 - - - -
279B THR* 3.2 17.0 - - - -
281B ASN 3.2 13.1 + - - -
282B LEU* 4.5 1.4 - - - +
380B VAL 3.1 9.7 + - - -
381B MET* 1.3 75.2 - - - +
383B ALA* 1.3 61.0 + - - -
384B VAL 3.1 3.1 - - - -
385B ILE* 2.8 19.0 + - - +
386B MET* 3.0 13.8 + - - +
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Residues in contact with ALA 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B TYR* 4.6 4.3 - - + -
202B LEU* 5.0 5.8 - - + -
276B ASP 4.2 1.2 + - - -
277B SER* 5.1 1.9 + - - +
279B THR 2.8 8.2 + - - +
280B THR* 3.1 14.7 + - + +
382B GLY* 1.3 71.3 - - - -
384B VAL* 1.3 56.2 + - - +
386B MET* 4.2 8.5 - - - +
387B GLU* 2.8 52.3 + - + +
501B 0GH 3.5 31.9 - - + -
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Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B THR* 3.0 17.7 + - + +
281B ASN* 3.9 0.7 - - - -
282B LEU* 3.9 22.7 - - + +
348B ILE* 3.9 16.9 - - + +
352B GLN* 3.3 44.2 - - - +
353B TYR* 3.8 18.8 - - + -
355B ARG* 5.9 0.7 - - + -
371B ALA* 3.4 42.2 - - + +
382B GLY 3.1 0.6 + - - -
383B ALA* 1.3 76.4 - - - +
385B ILE* 1.3 61.6 + - - +
387B GLU* 4.3 2.8 + - - +
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Residues in contact with ILE 385 (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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275B VAL* 6.1 0.2 - - + -
282B LEU* 3.9 26.5 - - + -
331B ILE* 6.5 0.2 - - + -
333B LEU* 3.9 23.3 - - + -
346B ILE* 4.1 13.9 - - + -
348B ILE* 4.1 26.7 - - + -
381B MET* 3.6 44.2 - - + -
382B GLY 2.8 10.1 + - - +
384B VAL* 1.3 77.3 - - - +
386B MET* 1.3 64.1 + - + +
388B GLY* 3.0 17.8 + - - -
389B PHE* 3.1 23.1 - - + -
402B PHE* 4.5 6.7 - - + -
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Residues in contact with MET 386 (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* 4.0 25.9 - - + +
202B LEU* 3.8 27.1 + - + +
275B VAL* 3.9 22.2 - - + -
276B ASP 4.3 2.2 - - - -
277B SER* 3.8 30.3 - - - -
381B MET 4.3 2.7 - - - +
382B GLY 3.0 11.4 + - - +
383B ALA* 4.2 2.2 - - - +
385B ILE* 1.3 80.5 - - + +
387B GLU* 1.3 58.5 + - - +
388B GLY 3.0 0.9 - - - -
389B PHE 2.9 26.5 - - - +
391B VAL* 4.1 23.3 - - + -
393B PHE* 3.9 27.8 - - + -
402B PHE* 6.0 0.2 - - + -
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Residues in contact with GLU 387 (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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58B SER* 2.9 30.3 + - - -
62B TYR* 2.7 37.9 + - + +
202B LEU* 3.3 18.7 - - + +
204B GLY* 3.8 15.8 + - - +
351B GLN 5.3 2.1 - - - +
352B GLN* 4.5 20.5 - - + +
355B ARG* 6.1 0.3 - - - +
383B ALA* 2.8 34.2 + - + +
384B VAL* 4.8 3.5 - - - +
385B ILE 3.2 0.2 + - - -
386B MET* 1.3 71.0 - - - +
388B GLY* 1.3 59.1 + - - +
389B PHE 4.9 0.2 - - - -
405B SER* 4.5 2.9 - - - -
407B CYS 4.8 1.0 - - - +
408B HIS* 3.5 19.9 + - - +
409B VAL* 4.8 0.6 + - + -
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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
------------------------------------------------------------
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