Contacts of the strand formed by residues 116 - 121 (chain B) in PDB entry 1GMO
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 PHE 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B LYS* 2.8 22.2 + - - -
48B THR 2.9 22.2 - - - +
49B THR* 3.2 33.7 - - + -
88B VAL* 3.9 14.8 - - + -
89B PHE 3.6 0.4 - - - -
90B ASP* 2.8 34.8 - - + -
91B LYS* 4.1 1.0 + - - -
93B ARG* 5.1 2.7 - - - -
97B LEU* 5.2 9.4 - - + -
112B PHE 5.2 0.7 - - - -
113B GLY* 2.8 22.4 + - - +
115B GLU* 1.3 102.2 - - + +
117B ASP* 1.3 73.4 + - - +
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Residues in contact with ASP 117 (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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44B LYS* 3.0 32.7 + - - -
45B SER 4.1 3.1 - - - -
46B ALA* 3.6 2.8 - - - +
47B LYS 3.1 9.9 + - - -
48B THR 4.0 1.1 - - - -
88B VAL* 3.3 3.7 - - - +
89B PHE* 3.0 33.4 + - + +
91B LYS* 2.9 34.7 + - - -
116B PHE* 1.3 91.9 - - - +
118B LEU* 1.3 59.1 + - - +
119B TYR* 3.0 33.1 + - + +
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Residues in contact with LEU 118 (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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43B LYS 3.6 1.0 - - - +
44B LYS* 3.3 4.0 - - - +
45B SER* 2.7 54.7 + - - +
48B THR* 3.6 26.8 + - + +
50B LEU* 3.3 31.4 - - + -
86B ALA* 4.4 10.5 - - + -
87B PHE 4.0 4.0 - - - +
88B VAL* 3.7 23.1 - - + -
99B PHE* 5.1 0.2 - - + -
103B SER* 4.5 0.2 - - - -
110B LYS* 4.5 8.3 - - - -
117B ASP* 1.3 70.4 - - - +
119B TYR* 1.3 66.3 + - - +
120B GLU* 3.9 32.1 - - + +
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Residues in contact with TYR 119 (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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39B ILE* 4.1 25.5 - - + +
42B PHE* 3.6 24.1 - - + -
43B LYS 3.9 3.4 - - - -
44B LYS* 3.7 41.0 + - + +
67B ALA* 4.0 17.2 - - + +
86B ALA* 3.1 3.7 - - - -
87B PHE* 2.8 74.9 + + + +
89B PHE* 4.3 6.8 - - + -
117B ASP* 3.0 45.3 + - + +
118B LEU* 1.3 73.9 - - - +
120B GLU* 1.3 63.4 + - - +
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Residues in contact with GLU 120 (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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42B PHE* 3.4 3.5 - - - -
43B LYS* 2.9 59.4 + - - +
45B SER* 4.8 4.3 + - - -
85B LYS 3.9 4.5 - - - +
86B ALA* 3.9 8.7 - - + -
102B ASN* 3.5 8.1 - - + +
103B SER* 2.4 46.9 + - - +
104B MET* 4.5 2.6 - - - +
118B LEU* 3.9 24.8 - - + +
119B TYR* 1.3 75.7 - - - +
121B ASN* 1.3 65.2 + - - +
122B LYS 3.3 1.4 + - - -
125B ILE* 3.8 18.6 - - + +
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Residues in contact with ASN 121 (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 GLU 4.8 1.4 - - - +
42B PHE* 3.8 26.5 - - + -
74B CYS* 4.6 7.5 + - - -
75B THR* 5.4 3.4 + - - +
84B CYS 3.4 16.5 + - - +
85B LYS 2.8 27.5 + - - +
102B ASN* 5.1 0.3 + - - -
120B GLU* 1.3 70.1 - - - +
122B LYS* 1.3 65.0 + - - +
123B ASP* 2.9 38.9 + - - +
124B TYR* 3.1 30.4 + - + +
125B ILE* 3.5 10.3 - - - +
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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