Contacts of the strand formed by residues 108 - 121 (chain B) in PDB entry 1GP9
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 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B LEU* 4.4 12.1 - - + -
51B ILE 3.2 16.8 - - - +
52B LYS* 4.0 1.1 - - - -
53B ILE* 4.5 2.5 - - - -
57B LEU* 3.8 9.2 - - + -
101B PHE* 3.7 39.5 - - + -
102B ASN 3.3 23.3 - - - +
103B SER* 4.4 8.6 - - - +
105B SER* 2.9 20.3 + - - +
106B SER* 2.9 6.0 + - - +
107B GLY* 1.3 86.4 - - - +
109B LYS* 1.3 72.8 + - - +
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Residues in contact with LYS 109 (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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50B LEU* 3.8 6.7 - - - +
51B ILE* 3.1 34.0 + - + +
53B ILE* 3.6 28.2 - - + +
103B SER 6.1 0.2 - - - -
108B VAL* 1.3 79.9 - - - +
110B LYS* 1.3 65.6 + - - +
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B SER* 5.2 6.5 + - - -
48B THR* 3.7 20.0 - - + +
49B THR 3.5 14.8 - - - +
50B LEU* 3.6 6.5 - - + -
51B ILE* 5.6 0.2 - - - -
103B SER* 3.2 40.8 + - - +
109B LYS* 1.3 78.1 - - - +
111B GLU* 1.3 61.8 + - - +
118B LEU* 4.9 4.6 - - - +
120B GLU* 5.5 0.8 + - - -
1210B EPE 6.3 3.1 - - - -
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Residues in contact with GLU 111 (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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47B LYS 4.9 0.4 - - - -
48B THR* 4.2 3.1 - - - -
49B THR* 3.3 42.4 + - + +
50B LEU* 5.1 0.2 - - - +
51B ILE* 2.9 34.8 - - + +
109B LYS 4.2 0.4 + - - -
110B LYS* 1.3 77.5 - - - +
112B PHE* 1.3 72.5 + - - +
116B PHE* 5.9 1.7 - - - -
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Residues in contact with PHE 112 (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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47B LYS* 3.6 34.8 - - + -
48B THR* 5.9 0.2 - - - -
49B THR* 5.1 0.2 - - - +
111B GLU* 1.3 89.7 - - - +
113B GLY* 1.3 73.5 + - - +
114B HIS* 3.6 48.9 - + - -
116B PHE* 5.0 1.7 - - - -
1210B EPE 4.2 15.7 - - - -
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Residues in contact with GLY 113 (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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47B LYS* 3.0 26.4 + - - -
111B GLU 3.8 0.4 + - - -
112B PHE* 1.3 85.0 - - - +
114B HIS* 1.3 65.7 + - - -
115B GLU* 3.2 7.2 - - - -
116B PHE* 3.2 25.9 + - - +
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Residues in contact with HIS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LYS* 2.8 61.7 + - + +
91B LYS* 3.4 18.4 + - - -
112B PHE* 3.6 27.1 - + - -
113B GLY* 1.3 72.4 - - - +
115B GLU* 1.3 60.7 + - - +
116B PHE 3.2 3.5 + - - -
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Residues in contact with GLU 115 (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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89B PHE 3.4 0.5 - - - +
90B ASP* 3.2 22.9 - - - +
91B LYS* 2.9 35.8 + - + +
92B ALA* 3.6 24.2 - - + +
93B ARG* 3.2 28.4 + - - +
113B GLY* 3.5 6.1 - - - -
114B HIS* 1.3 84.3 + - - +
116B PHE* 1.3 73.1 + - + +
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Residues in contact with PHE 116 (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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47B LYS* 2.7 33.1 + - - -
48B THR 2.9 19.3 + - - +
49B THR* 3.7 25.8 - - + -
88B VAL* 3.9 16.6 - - + -
89B PHE 3.5 2.0 - - - -
90B ASP* 3.0 30.7 - - + -
91B LYS* 4.1 0.5 + - - -
93B ARG* 4.6 5.8 - - - -
95B GLN* 6.0 0.7 - - - -
97B LEU* 4.9 7.6 - - + -
111B GLU* 5.9 1.6 - - - -
112B PHE 5.2 1.3 - - - -
113B GLY* 3.6 25.1 - - - +
114B HIS 3.2 3.8 + - - -
115B GLU* 1.3 105.0 - - - +
117B ASP* 1.3 63.3 - - - +
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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* 3.8 23.3 + - + -
45B SER 3.8 2.9 - - - +
46B ALA* 2.9 28.6 - - - +
47B LYS* 3.1 2.1 + - - +
48B THR 3.6 2.5 - - - -
88B VAL* 3.1 4.5 - - - -
89B PHE* 2.8 36.8 + - + +
91B LYS* 2.9 31.0 + - + +
116B PHE* 1.3 76.6 - - - +
118B LEU* 1.3 61.7 + - - +
119B TYR* 3.6 26.0 + - + +
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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 3.7 0.3 - - - +
44B LYS* 3.1 6.2 - - - +
45B SER* 2.8 53.5 + - - +
48B THR* 3.3 25.5 + - + +
50B LEU* 4.0 37.0 - - + -
86B ALA* 4.1 17.0 - - + -
87B PHE 3.7 5.2 - - - +
88B VAL* 3.6 19.1 - - + -
99B PHE* 5.0 0.2 - - + -
103B SER* 4.4 6.7 - - - -
110B LYS* 4.9 1.6 - - - +
117B ASP* 1.3 74.0 - - - +
119B TYR* 1.3 71.2 + - - +
120B GLU* 4.2 21.8 - - + +
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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 VAL* 3.3 33.1 - - + +
42B PHE* 3.7 16.7 - - + -
43B LYS 3.6 2.9 - - - -
44B LYS* 3.8 38.6 + - + +
67B ALA* 3.8 23.3 - - + +
86B ALA* 3.3 3.5 - - - -
87B PHE* 2.8 75.0 + + + +
89B PHE* 4.4 2.2 - - + -
117B ASP* 3.6 38.6 + - + +
118B LEU* 1.3 75.5 - - - +
120B GLU* 1.3 63.2 + - - +
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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* 3.1 7.6 - - - -
43B LYS* 2.7 60.1 + - + +
45B SER* 4.3 10.9 + - - -
85B LYS 4.4 2.9 - - - +
86B ALA* 4.0 9.2 - - + -
102B ASN* 3.3 20.3 - - + +
103B SER* 2.7 42.8 + - - -
104B MET* 4.4 5.3 + - - +
110B LYS* 5.5 0.7 + - - -
118B LEU* 4.2 13.6 - - + +
119B TYR* 1.3 72.3 - - - +
121B ASN* 1.3 63.1 + - - +
122B LYS 3.5 0.7 + - - -
125B ILE* 3.9 18.1 - - + +
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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* 3.4 21.9 - - - +
42B PHE* 3.2 30.1 - - + -
74B CYS* 5.5 1.0 + - - -
75B THR* 4.7 8.2 + - - +
84B CYS 4.5 12.8 + - - +
85B LYS 3.7 10.7 + - - +
119B TYR 4.0 0.2 + - - -
120B GLU* 1.3 71.3 - - - +
122B LYS* 1.3 72.2 + - - +
123B ASP* 2.9 43.6 + - - +
124B TYR* 2.9 29.5 + - + +
125B ILE* 3.7 9.6 - - - +
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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