Contacts of the strand formed by residues 103 - 118 (chain B) in PDB entry 5GKF
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B TYR* 2.2 34.7 + - + -
42B ASP 3.4 5.2 - - - -
43B GLY* 3.5 6.1 - - - -
44B ARG* 2.9 31.4 + - - +
78B GLN* 2.4 41.3 + - - +
96B SER 3.8 0.3 - - - +
97B ILE* 3.6 4.9 - - - +
98B ARG* 2.7 51.7 + - - +
101B PRO* 3.2 14.6 + - + +
102B ARG* 1.3 82.6 - - - +
104B THR* 1.3 61.0 + - - +
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Residues in contact with THR 104 (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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40B HIS 4.7 2.2 - - - +
41B TYR* 3.5 7.7 - - - -
42B ASP* 2.5 46.4 + - + +
78B GLN* 4.6 1.3 - - - -
95B VAL* 5.3 3.0 - - + +
96B SER 3.3 2.9 - - - +
97B ILE* 3.4 24.4 - - - +
103B GLU* 1.3 72.2 + - - +
105B LEU* 1.3 69.5 + - - +
106B GLU* 4.3 22.7 - - + +
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 3.6 31.2 - - + -
40B HIS 3.7 4.9 - - - +
41B TYR* 4.1 15.3 - - + -
64B PHE* 3.9 18.5 - - + -
66B ILE* 3.8 15.5 - - + -
76B ASN* 4.1 5.8 - - + -
77B TRP* 3.4 40.2 - - - +
78B GLN* 3.7 12.7 + - + +
94B LEU 3.7 1.4 - - - +
95B VAL* 3.4 4.5 - - - +
96B SER* 2.8 48.7 + - - -
104B THR* 1.3 75.0 - - - +
106B GLU* 1.3 62.1 + - - +
107B VAL* 4.7 1.3 - - + -
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Residues in contact with GLU 106 (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 5.6 - - - +
40B HIS* 2.6 69.3 + - + +
89B ARG* 4.0 18.9 + - - -
93B VAL* 4.1 9.4 - - + +
94B LEU 3.6 2.2 - - - -
95B VAL* 3.8 22.9 - - + +
104B THR* 4.3 18.5 - - + +
105B LEU* 1.3 73.6 - - - +
107B VAL* 1.3 63.3 + - - +
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B CYS* 4.0 16.4 - - + -
38B LYS 3.7 2.7 - - - +
39B VAL* 4.1 8.5 - - + -
56B ILE* 4.1 11.9 - - + -
64B PHE* 3.7 15.9 - - + -
66B ILE* 3.7 34.5 - - + -
93B VAL* 3.3 4.4 - - - -
94B LEU* 2.8 50.6 + - + +
105B LEU* 4.1 1.3 - - + -
106B GLU* 1.3 76.2 - - - +
108B GLU* 1.3 62.3 + - - +
109B LEU* 3.7 24.4 + - + +
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Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B CYS* 3.2 24.8 - - - -
38B LYS* 2.8 35.9 + - + +
40B HIS* 3.9 20.9 + - + +
91B ASN* 2.7 35.7 + - + +
92B PRO 3.7 2.7 - - - -
93B VAL* 3.8 21.5 - - + -
106B GLU 4.0 0.6 + - - -
107B VAL* 1.3 72.5 - - - +
109B LEU* 1.3 60.5 + - - +
110B GLU* 3.3 12.3 + - - +
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Residues in contact with LEU 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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17B LEU* 4.4 7.0 - - + -
21B VAL* 6.1 0.4 - - + -
33B ILE* 4.7 17.0 - - + -
35B ALA* 3.9 22.7 - - + -
36B ARG 4.1 3.1 - - - -
37B CYS* 4.6 1.1 - - + -
56B ILE* 4.4 7.6 - - + -
86B LEU* 4.7 9.0 - - + -
91B ASN* 3.3 19.5 - - - +
92B PRO* 3.0 40.4 + - + +
94B LEU* 4.9 10.8 - - + -
107B VAL* 3.8 27.4 - - + +
108B GLU* 1.3 68.9 - - - +
110B GLU* 1.3 64.4 + - - +
111B GLU* 4.6 0.2 - - - -
112B VAL* 3.8 26.4 + - + -
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Residues in contact with GLU 110 (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 ARG* 3.0 45.3 + - + +
37B CYS 4.5 2.0 - - - -
38B LYS* 3.0 39.8 - - - +
51B SER* 2.5 25.0 + - - -
91B ASN* 4.3 15.1 - - - +
108B GLU* 4.0 20.0 - - - +
109B LEU* 1.3 76.4 - - - +
111B GLU* 1.3 63.3 + - - +
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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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11B SER* 5.4 5.9 + - - -
35B ALA* 3.1 5.3 - - - +
36B ARG* 2.8 73.4 + - + +
110B GLU* 1.3 80.7 - - - +
112B VAL* 1.3 69.8 + - - +
113B TYR* 3.6 25.9 + - + -
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Residues in contact with VAL 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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11B SER* 3.8 5.2 - - - -
12B PRO* 3.2 37.1 - - + +
17B LEU* 4.3 16.2 - - + -
33B ILE* 4.0 9.0 - - + -
34B PHE 3.8 2.7 - - - -
35B ALA* 3.9 5.6 - - + -
92B PRO* 5.8 0.7 - - + -
109B LEU* 3.8 37.0 - - + -
111B GLU* 1.3 77.9 - - - +
113B TYR* 1.3 60.3 + - - +
114B MET 3.5 29.4 - - - +
115B VAL* 4.1 5.2 - - + +
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Residues in contact with TYR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 3.4 36.5 + - + +
6A VAL* 3.6 22.7 - - + +
118A PHE* 3.7 11.7 - + - -
10B THR* 3.1 10.6 - - - +
11B SER* 2.9 26.2 + - - +
12B PRO* 4.2 0.4 - - - -
34B PHE 2.8 24.5 + - - +
35B ALA* 3.7 2.5 - - - -
36B ARG* 3.6 33.3 + - + +
53B ASP* 2.9 33.7 + - - -
111B GLU* 4.0 29.3 + - + -
112B VAL* 1.3 73.9 - - - +
114B MET* 1.3 58.7 + - - +
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Residues in contact with MET 114 (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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6A VAL* 4.5 2.7 - - + -
8A VAL* 4.2 9.6 - - + -
34A PHE* 5.5 1.1 - - + -
114A MET* 4.7 7.2 - - - +
8B VAL* 3.6 28.0 - - + -
9B ILE 3.3 12.3 - - - +
10B THR* 4.1 11.9 - - + -
32B THR* 3.2 32.1 - - + +
33B ILE* 3.1 13.4 - - - +
34B PHE* 2.9 68.1 + - + -
112B VAL* 3.7 4.5 - - - -
113B TYR* 1.3 80.4 - - - +
115B VAL* 1.3 61.2 + - - +
116B SER* 3.4 16.4 - - - +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 3.6 1.7 - - - +
9B ILE* 3.0 30.9 + - + +
12B PRO* 3.5 32.1 - - + -
17B LEU* 4.1 14.1 - - + -
20B LEU* 3.8 34.6 - - + +
21B VAL* 4.2 11.2 - - + -
31B LEU* 4.0 13.5 - - + -
32B THR 3.5 4.0 - - - -
33B ILE* 3.9 17.9 - - + -
112B VAL* 4.4 0.9 - - + -
114B MET* 1.3 75.4 - - - +
116B SER* 1.3 67.8 + - - +
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Residues in contact with SER 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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34A PHE* 3.5 19.6 - - - -
114A MET* 5.0 0.2 - - - -
7B THR 3.1 12.1 - - - -
8B VAL* 4.2 6.5 - - - -
20B LEU* 4.8 0.9 - - - -
30B MET 3.6 0.2 - - - +
31B LEU* 3.5 9.6 - - - +
32B THR* 2.9 48.1 + - - -
114B MET* 3.4 15.9 - - - +
115B VAL* 1.3 80.9 - - - +
117B VAL* 1.3 65.8 + - - +
118B PHE 4.2 0.2 - - - -
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Residues in contact with VAL 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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34A PHE* 5.1 0.2 - - - -
5B LYS 3.2 1.7 - - - +
6B VAL* 3.2 8.0 - - - +
7B THR* 2.9 34.1 + - - +
20B LEU* 3.9 35.2 - - + +
23B SER* 4.2 3.1 - - - +
24B ALA* 3.8 26.0 - - + -
27B GLU* 4.9 0.2 - - - +
29B ALA* 3.8 24.2 - - + -
30B MET 3.5 2.5 - - - +
31B LEU* 4.6 0.7 - - + -
116B SER* 1.3 79.2 - - - +
118B PHE* 1.3 62.7 + - - +
119B ARG* 3.8 29.9 + - + +
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Residues in contact with PHE 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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34A PHE* 3.7 40.2 - + + -
35A ALA 4.1 0.2 - - - -
53A ASP* 3.7 20.2 - - + -
54A ARG* 3.4 32.3 - - - -
55A VAL* 3.8 14.8 - - + -
113A TYR* 3.6 29.6 - + - -
5B LYS* 3.3 13.9 - - + -
6B VAL* 4.1 8.3 - - + +
29B ALA* 4.3 0.2 - - - -
30B MET* 2.9 43.9 + - + +
32B THR* 5.5 0.4 - - - +
117B VAL* 1.3 74.2 - - - +
119B ARG* 1.3 63.1 + - - +
120B ALA* 3.3 27.1 + - + -
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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