Contacts of the helix formed by residues 85 - 90 (chain A) in PDB entry 2GAO
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 85 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE* 4.7 14.1 - - + -
84A ARG* 1.3 76.2 - - - +
86A TRP* 1.3 63.4 + - - +
87A LYS 2.9 6.9 + - - -
88A ASN* 2.9 38.5 + - + +
89A TYR* 4.2 6.6 + - + -
55B PRO* 3.8 22.7 - - + -
57B LEU 3.9 21.3 - - - +
58B HIS* 5.3 4.7 - - + -
59B PRO* 5.8 4.7 - - + -
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Residues in contact with TRP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 5.2 3.5 - - + +
31A LEU* 4.0 20.6 - - + -
74A PHE* 3.2 53.5 - + + -
75A ASP 4.7 5.6 + - - -
76A LEU* 3.2 33.7 - - + +
84A ARG* 4.0 20.7 - - - +
85A VAL* 1.3 76.7 - - - +
87A LYS* 1.3 86.3 + - + +
89A TYR* 3.3 21.7 + - - +
90A LEU* 3.5 38.5 + - + +
118A LEU* 3.7 23.6 - - + -
121A ASP* 5.8 1.6 - - - -
124A ILE* 4.8 3.1 - - + -
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Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 3.3 45.3 - - + +
85A VAL 2.9 0.8 + - - -
86A TRP* 1.3 107.4 - - + +
88A ASN* 1.4 64.8 + - - +
89A TYR 3.2 0.4 - - - -
90A LEU* 3.3 33.5 + - + +
91A PRO* 3.9 4.0 - - - +
121A ASP* 3.9 20.1 + - - -
123A THR* 6.1 0.2 - - - -
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Residues in contact with ASN 88 (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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84A ARG 5.2 1.1 - - - +
85A VAL* 2.9 37.4 + - + +
87A LYS* 1.4 78.0 - - - +
89A TYR* 1.3 64.8 + - + +
91A PRO* 3.6 11.1 - - - +
55B PRO* 4.3 14.3 - - - +
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Residues in contact with TYR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 5.4 10.8 - - + -
29A VAL* 6.0 1.8 - - + -
63A GLU* 2.8 31.2 + - - -
70A THR* 5.5 3.1 - - + -
72A THR* 3.6 22.6 - - + +
74A PHE* 3.7 26.4 - + + -
85A VAL* 4.5 9.6 - - + -
86A TRP 3.3 11.5 + - - +
87A LYS 3.2 0.2 - - - -
88A ASN* 1.3 83.9 - - + +
90A LEU* 1.3 64.3 + - - +
91A PRO* 3.0 2.2 - - - +
92A ALA* 2.9 21.5 + - - +
93A ILE* 3.6 28.1 + - + +
46B LYS* 3.9 20.3 + - - +
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 5.3 3.6 - - + -
86A TRP* 3.5 36.6 - - + +
87A LYS* 3.3 37.7 + - + +
89A TYR* 1.3 75.7 - - - +
91A PRO* 1.3 68.8 - - + +
93A ILE* 3.0 32.8 + - + +
96A ILE* 4.9 7.6 - - + -
121A ASP* 5.3 2.5 - - - +
123A THR* 4.3 13.0 - - - +
124A ILE* 3.5 40.6 - - + +
127A VAL* 5.2 2.3 - - - +
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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