Contacts of the strand formed by residues 129 - 134 (chain B) 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 ILE 129 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ILE* 3.4 24.0 - - + +
98B PHE* 4.3 7.6 - - + -
115B LEU* 4.2 13.7 - - + -
118B LEU* 4.8 13.5 - - + +
119B MET* 4.3 19.7 - - + -
124B ILE* 6.3 0.2 - - + -
127B VAL 3.7 4.9 - - - +
128B PRO* 1.3 77.0 - - - +
130B LEU* 1.3 65.5 + - - +
131B ILE* 3.8 21.5 - - + -
171B ARG* 3.7 34.3 - - - +
172B PRO 3.0 9.5 + - - -
173B MET* 3.2 15.5 - - + +
174B GLU 3.2 24.3 + - - -
192B TRP* 3.5 4.9 - - - -
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Residues in contact with LEU 130 (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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96B ILE 2.8 11.3 + - - +
97B VAL* 3.2 26.1 - - + -
98B PHE* 2.7 33.3 + - - +
128B PRO 4.1 0.6 - - - -
129B ILE* 1.3 71.4 - - - +
131B ILE* 1.3 66.6 + - - +
132B LEU* 3.7 18.8 - - + -
174B GLU 3.9 0.9 - - - +
176B PHE* 3.5 33.4 - - + -
189B GLY* 3.4 30.7 - - - +
190B PHE* 3.8 13.0 - - + +
192B TRP* 3.8 13.4 - - + -
193B LEU* 4.1 11.8 - - + +
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 3.3 15.3 - - + +
100B VAL* 4.2 20.2 - - + -
115B LEU* 3.9 22.4 - - + -
129B ILE* 3.8 15.7 - - + -
130B LEU* 1.3 77.7 - - - +
132B LEU* 1.3 58.5 + - - +
133B GLY 3.9 0.3 + - - -
147B LEU* 5.0 5.8 - - + -
151B PHE* 5.7 1.1 - - + -
153B LEU* 3.8 27.6 - - + -
157B THR* 5.1 0.4 - - + -
173B MET* 3.8 25.8 - - + -
174B GLU 2.9 14.1 + - - +
175B VAL* 3.4 17.2 - - + +
176B PHE 2.8 30.7 + - - +
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Residues in contact with LEU 132 (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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41B LEU* 3.7 29.8 - - + -
97B VAL* 3.7 19.5 - - + -
98B PHE 2.8 9.5 + - - +
99B LEU* 3.5 15.0 - - + -
100B VAL* 2.9 30.1 + - - +
130B LEU* 3.7 24.4 + - + -
131B ILE* 1.3 72.6 - - - +
133B GLY* 1.3 60.1 + - - +
134B ASN 3.3 2.0 + - - +
176B PHE* 3.3 19.1 - - + +
178B CYS* 3.9 15.7 - - - -
180B VAL* 5.0 0.7 - - + -
186B TYR* 3.9 32.1 - - + +
190B PHE* 4.4 4.3 - - + -
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Residues in contact with GLY 133 (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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100B VAL* 3.9 1.3 - - - -
102B CYS* 3.6 22.0 - - - -
131B ILE 3.9 1.0 + - - -
132B LEU* 1.3 69.2 - - - +
134B ASN* 1.3 60.0 + - - -
136B ILE* 3.4 10.7 - - - +
147B LEU* 3.7 16.8 - - - +
175B VAL* 5.2 0.2 - - - +
176B PHE 2.9 13.4 + - - -
177B MET* 3.4 5.4 - - - -
178B CYS 3.0 26.1 + - - +
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Residues in contact with ASN 134 (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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36B ALA 2.9 26.6 + - - +
37B GLY* 3.9 5.3 - - - -
99B LEU* 4.2 8.6 - - + +
100B VAL 2.8 16.5 + - - +
102B CYS* 3.0 23.7 + - - +
132B LEU 3.3 3.8 + - - +
133B GLY* 1.3 73.6 - - - +
135B LYS* 1.3 88.5 + - - +
136B ILE 3.4 1.6 - - - -
178B CYS* 3.3 11.6 - - - -
180B VAL* 3.0 38.5 + - - +
501B GDP 3.2 25.1 + - - +
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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