Contacts of the helix formed by residues 64 - 68 (chain A) in PDB entry 3GSB
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 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ASP* 2.9 7.1 + - - +
63A TYR* 1.3 80.4 - - - +
65A GLY* 1.3 54.9 + - - +
66A THR* 4.1 3.6 - - - +
67A TRP* 2.8 70.5 + - + +
399A TYR* 3.8 22.7 - - + -
400A LEU* 3.5 8.3 - - - -
401A ALA* 3.2 39.9 - - + +
402A PRO* 5.1 0.7 - - + -
409A PHE* 3.4 16.7 - - - -
93B PHE 5.6 2.0 - - - +
94B GLY* 5.6 1.6 - - - -
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Residues in contact with GLY 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASP* 3.0 15.0 + - - -
63A TYR 3.8 1.0 - - - +
64A VAL* 1.3 75.2 - - - +
66A THR* 1.3 74.8 + - - +
68A GLY* 3.0 12.5 + - - -
70A ALA* 3.4 25.1 + - - +
74A HIS* 4.2 9.6 - - - -
252A ARG* 5.5 0.8 + - - -
409A PHE* 5.1 4.2 - - - +
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Residues in contact with THR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASP* 5.0 1.2 + - - -
64A VAL* 3.4 3.8 - - - +
65A GLY* 1.3 85.0 - - - +
67A TRP* 1.3 67.7 + - - +
69A PRO* 3.1 35.1 - - + +
70A ALA* 4.1 7.6 - - + +
74A HIS* 4.4 4.8 + - + +
278A GLY* 5.8 0.2 - - - -
92B SER* 3.0 43.8 + - - +
93B PHE 3.4 23.6 + - - -
94B GLY* 3.4 17.5 + - - -
305B THR* 3.5 12.8 + - - +
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Residues in contact with TRP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 3.6 26.7 - - + -
32A ARG* 5.4 0.9 - - - -
64A VAL* 2.8 30.9 + - + +
66A THR* 1.3 83.5 - - - +
68A GLY* 1.3 55.1 + - - +
69A PRO* 3.6 0.4 - - - -
248A MET* 4.6 1.3 - - + +
273A LYS* 3.2 23.0 + - - +
399A TYR* 5.9 1.6 - + - -
401A ALA* 3.9 14.1 - - + -
402A PRO* 3.8 30.7 - - + -
403A SER* 5.9 0.9 - - - -
406A GLU* 3.7 31.4 - - + -
409A PHE* 4.0 23.7 - + + -
500A GAB 2.5 62.0 + + + +
94B GLY* 3.1 25.4 + - - -
305B THR* 4.2 6.1 - - + -
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Residues in contact with GLY 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL 3.6 3.8 + - - -
65A GLY* 3.0 8.0 + - - -
67A TRP* 1.3 80.4 - - - +
69A PRO* 1.3 61.9 - - - +
70A ALA 3.3 2.2 - - - -
248A MET* 5.8 1.3 - - - -
252A ARG* 2.8 34.8 + - - -
273A LYS* 4.3 9.0 - - - -
274A ILE* 3.0 13.5 - - - +
409A PHE* 4.2 8.6 - - - -
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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
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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