Contacts of the strand formed by residues 103 - 118 (chain A) in PDB entry 5GKI
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 GLU 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A TYR* 2.5 35.2 + - + -
42A ASP 3.4 4.7 - - - +
43A GLY* 3.8 6.1 - - - -
44A ARG* 3.1 39.2 + - - +
78A GLN* 3.5 20.6 + - - +
97A ILE* 3.4 8.1 - - - +
98A ARG* 2.8 59.5 + - + +
101A PRO* 3.3 13.4 + - + +
102A ARG* 1.3 82.3 - - - +
104A THR* 1.3 64.1 + - - +
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Residues in contact with THR 104 (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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40A HIS 3.8 0.8 - - - +
41A TYR* 3.4 7.9 - - - -
42A ASP* 2.6 46.4 + - + +
78A GLN* 4.5 0.2 - - - -
95A VAL* 5.0 6.3 - - + -
96A SER 3.6 3.6 - - - +
97A ILE* 4.2 16.1 - - + +
102A ARG* 4.5 10.4 + - - +
103A GLU* 1.3 75.9 + - - +
105A LEU* 1.3 63.4 + - - +
106A GLU* 3.8 29.6 - - + +
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Residues in contact with LEU 105 (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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39A VAL* 3.7 21.8 - - + -
40A HIS 3.6 12.1 - - - +
41A TYR* 3.8 18.4 - - + -
64A PHE* 3.8 25.2 - - + -
66A ILE* 4.1 9.0 - - + -
76A ASN* 4.1 6.3 - - + -
77A TRP* 3.5 35.2 - - - +
78A GLN* 3.7 21.7 - - + +
94A LEU 3.7 0.9 - - - +
95A VAL* 3.4 4.0 - - - +
96A SER* 2.8 41.8 + - - +
104A THR* 1.3 72.6 - - - +
106A GLU* 1.3 61.5 + - - +
107A VAL* 4.2 4.9 - - + +
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Residues in contact with GLU 106 (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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38A LYS 3.7 0.9 - - - +
39A VAL* 3.5 3.9 - - - -
40A HIS* 2.8 62.9 + - + +
89A ARG* 3.1 39.2 + - - -
93A VAL* 4.1 5.5 - - + +
94A LEU 3.4 3.1 - - - -
95A VAL* 4.0 13.2 - - + +
104A THR* 3.8 20.8 - - + +
105A LEU* 1.3 78.0 - - - +
107A VAL* 1.3 63.2 + - - +
108A GLU 4.0 0.2 - - - -
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Residues in contact with VAL 107 (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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37A CYS* 3.8 15.7 - - + -
38A LYS 3.5 9.0 - - - +
39A VAL* 4.1 6.5 - - + -
56A ILE* 3.7 27.8 - - + -
64A PHE* 3.6 29.8 - - + -
66A ILE* 3.6 22.0 - - + -
93A VAL* 3.1 4.1 - - - -
94A LEU* 2.7 47.8 + - + +
105A LEU* 4.6 3.1 - - + -
106A GLU* 1.3 75.5 - - - +
108A GLU* 1.3 62.4 + - - +
109A LEU* 3.5 6.3 + - + +
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Residues in contact with GLU 108 (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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37A CYS* 3.1 25.7 - - - +
38A LYS* 2.9 41.7 + - + +
40A HIS* 3.9 16.2 + - + +
91A ASN* 3.3 36.2 + - + +
92A PRO 3.7 3.6 - - - -
93A VAL* 3.9 16.8 - - + +
106A GLU 3.9 1.6 + - - -
107A VAL* 1.3 69.4 - - - +
109A LEU* 1.3 60.7 + - - +
110A GLU* 3.3 13.3 + - + +
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Residues in contact with LEU 109 (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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17A LEU* 4.3 13.9 - - + -
21A VAL* 6.3 0.2 - - + -
33A ILE* 4.4 11.2 - - + -
35A ALA* 4.0 13.5 - - + -
36A ARG 3.9 3.6 - - - +
37A CYS* 4.3 1.8 - - + -
56A ILE* 3.8 28.7 - - + -
86A LEU* 4.6 7.6 - - + -
91A ASN* 3.4 18.2 - - - +
92A PRO* 2.8 29.6 + - + +
94A LEU* 4.1 25.4 - - + +
107A VAL* 3.9 18.2 - - + +
108A GLU* 1.3 70.7 - - - +
110A GLU* 1.3 61.8 + - - +
111A GLU* 3.6 0.9 - - - -
112A VAL* 3.8 25.4 - - + +
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Residues in contact with GLU 110 (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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36A ARG* 2.9 43.2 + - - +
37A CYS 3.9 7.2 - - - -
38A LYS* 3.6 30.1 + - - +
51A SER* 2.7 31.8 + - - -
91A ASN* 3.9 29.3 - - - +
108A GLU* 3.3 15.5 + - - +
109A LEU* 1.3 75.4 - - - +
111A GLU* 1.3 66.6 + - - +
112A VAL 4.4 0.2 - - - -
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Residues in contact with GLU 111 (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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11A SER* 6.1 1.4 - - - -
35A ALA* 3.3 3.3 - - - -
36A ARG* 2.8 64.3 + - + +
110A GLU* 1.3 80.0 - - - +
112A VAL* 1.3 69.2 + - - +
113A TYR* 3.5 25.3 + - + +
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Residues in contact with VAL 112 (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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11A SER* 3.6 6.6 - - - -
12A PRO* 3.2 45.2 - - + +
17A LEU* 3.8 27.8 - - + -
33A ILE* 4.2 6.7 - - + -
34A PHE 3.9 4.9 - - - +
35A ALA* 3.9 4.5 - - + -
92A PRO* 5.2 1.3 - - + -
109A LEU* 3.8 28.9 - - + +
111A GLU* 1.3 78.4 + - - +
113A TYR* 1.3 59.5 + - - +
114A MET 3.5 22.7 - - - +
115A VAL* 4.3 4.7 - - + +
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Residues in contact with TYR 113 (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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10A THR* 3.3 8.0 - - - +
11A SER* 2.9 23.5 + - - +
34A PHE 2.8 15.8 + - - +
35A ALA* 3.6 3.4 - - - -
36A ARG* 3.1 34.1 - - + +
53A ASP* 2.7 30.2 + - - -
111A GLU* 4.0 24.6 - - + +
112A VAL* 1.3 73.3 - - - +
114A MET* 1.3 61.7 + - - +
5B LYS* 2.6 42.2 + - + -
6B VAL* 3.5 23.2 - - + +
118B PHE* 3.5 20.0 - + - -
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Residues in contact with MET 114 (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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8A VAL* 3.9 24.9 - - + -
9A ILE 3.5 10.1 - - - +
10A THR* 4.1 7.2 - - + -
32A THR* 4.1 6.5 - - + +
33A ILE* 3.4 3.3 - - - -
34A PHE* 2.9 80.6 + - + +
112A VAL* 3.5 9.7 - - - +
113A TYR* 1.3 79.6 - - - +
115A VAL* 1.3 68.3 + - - +
116A SER* 3.6 26.9 - - - +
6B VAL* 4.2 7.0 - - + -
8B VAL* 4.1 17.5 - - - -
34B PHE* 5.4 0.7 - - + -
114B MET* 4.8 7.2 - - - +
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Residues in contact with VAL 115 (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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8A VAL* 3.5 0.9 - - - -
9A ILE* 3.0 42.0 + - + +
12A PRO* 3.8 21.1 - - + -
17A LEU* 4.1 22.7 - - + -
20A LEU* 3.5 34.9 - - + +
21A VAL* 4.7 1.1 - - + -
31A LEU* 4.1 11.2 - - + -
32A THR 3.5 4.3 - - - -
33A ILE* 4.0 17.9 - - + -
112A VAL* 4.4 2.0 - - + -
114A MET* 1.3 77.2 - - - +
116A SER* 1.3 66.7 + - - +
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Residues in contact with SER 116 (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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7A THR 3.1 13.0 - - - -
8A VAL* 4.0 11.4 - - - -
20A LEU* 4.1 1.8 - - - -
30A MET 3.5 2.1 - - - +
31A LEU* 3.5 6.9 - - - +
32A THR* 2.9 55.0 + - - -
114A MET* 3.6 12.9 - - - +
115A VAL* 1.3 80.2 - - - +
117A VAL* 1.3 64.8 + - - +
118A PHE 4.1 0.2 - - - -
34B PHE* 3.5 18.9 - - - -
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Residues in contact with VAL 117 (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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5A LYS 3.7 1.0 - - - +
6A VAL* 3.3 6.3 - - - +
7A THR* 2.9 40.6 + - - +
20A LEU* 3.5 47.5 - - + +
23A SER* 4.8 4.3 - - - +
24A ALA* 4.0 17.7 - - + +
29A ALA* 3.6 23.6 - - + -
30A MET 3.6 2.2 - - - -
31A LEU* 4.3 1.6 - - + -
116A SER* 1.3 76.7 - - - +
118A PHE* 1.3 61.6 + - - +
119A ARG* 4.0 22.9 + - + +
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Residues in contact with PHE 118 (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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5A LYS* 3.6 9.9 - - + -
6A VAL* 3.5 15.7 - - + -
29A ALA* 3.9 2.2 - - - -
30A MET* 3.0 40.8 + - + +
32A THR* 5.2 0.2 - - - +
117A VAL* 1.3 73.1 - - - +
119A ARG* 1.3 65.0 + - - +
120A ALA* 2.8 32.7 + - + -
34B PHE* 3.4 41.1 - + + -
35B ALA 4.1 0.9 - - - -
53B ASP* 3.5 22.9 - - + -
54B ARG 3.4 28.7 - - - -
55B VAL* 3.8 13.7 - - + -
113B TYR* 3.8 24.9 - + - -
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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