Contacts of the strand formed by residues 30 - 42 (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 MET 30 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ASP 5.9 0.2 - - - +
54A ARG* 5.8 1.1 - - - -
55A VAL* 3.5 33.4 - - + -
67A HIS* 4.8 2.9 - - + +
68A GLN 3.7 16.8 - - - +
69A SER* 3.7 26.0 - - - -
24B ALA* 4.8 1.3 - - - -
29B ALA* 1.3 71.0 - - - +
31B LEU* 1.3 62.2 + - - +
32B THR* 3.9 3.3 + - - +
57B ILE* 4.3 12.6 - - + -
58B VAL 3.7 4.7 - - - +
59B LYS* 4.1 18.4 - - + -
60B PRO* 3.9 17.7 - - + -
116B SER 3.6 0.9 - - - +
117B VAL* 3.5 5.5 - - - -
118B PHE* 2.9 48.8 + - + +
120B ALA* 4.3 14.8 - - + +
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Residues in contact with LEU 31 (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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20B LEU 4.4 1.1 - - - +
21B VAL* 3.8 39.9 - - + +
24B ALA* 4.0 18.6 - - + -
25B LEU* 5.3 6.3 - - + -
29B ALA 3.7 1.0 + - - +
30B MET* 1.3 71.7 - - - +
32B THR* 1.3 60.8 + - - +
33B ILE* 3.9 23.1 - - + -
56B ILE* 3.5 1.9 - - + +
57B ILE* 3.2 6.8 - - - +
58B VAL* 2.9 63.7 + - + +
94B LEU* 4.4 8.5 - - + -
115B VAL* 4.0 15.9 - - + -
116B SER 3.5 13.5 - - - +
117B VAL* 4.6 0.4 - - + -
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Residues in contact with THR 32 (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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32A THR* 4.9 3.8 - - + -
34A PHE* 3.4 27.4 - - + -
55A VAL* 4.7 6.5 - - + +
30B MET* 3.9 5.1 + - - +
31B LEU* 1.3 75.5 + - - +
33B ILE* 1.3 68.1 + - - +
34B PHE* 3.8 25.6 - - + -
55B VAL* 4.0 10.5 - - + -
56B ILE 3.2 7.9 - - - +
57B ILE* 4.1 13.5 - - + +
114B MET* 3.2 3.8 - - + +
116B SER* 2.9 48.9 + - - +
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Residues in contact with ILE 33 (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* 4.7 5.6 - - + -
21B VAL* 4.4 14.1 - - + -
31B LEU* 3.9 25.8 - - + -
32B THR* 1.3 78.9 - - - +
34B PHE* 1.3 82.4 + - - +
35B ALA* 3.8 15.0 + - + -
54B ARG 3.7 0.7 - - - +
55B VAL* 3.5 1.2 - - - -
56B ILE* 2.8 52.0 + - + +
94B LEU* 4.3 17.0 - - + -
109B LEU* 4.7 8.3 - - + -
112B VAL* 4.0 10.1 - - + -
114B MET* 3.1 13.7 - - - +
115B VAL* 3.9 13.7 - - + -
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Residues in contact with PHE 34 (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* 4.0 12.6 - - + -
32A THR* 3.6 17.9 - - + -
114A MET* 5.4 1.3 - - + -
116A SER* 3.5 31.0 - - - -
118A PHE* 3.5 42.0 - + + -
32B THR* 3.8 12.3 - - + -
33B ILE* 1.3 77.9 - - - +
35B ALA* 1.3 54.8 + - - +
54B ARG 3.7 3.6 - - - -
55B VAL* 3.6 35.7 - - + -
112B VAL* 3.7 0.5 - - - -
113B TYR* 2.8 34.9 + - + -
114B MET* 2.9 47.7 + - + +
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Residues in contact with ALA 35 (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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118A PHE* 4.1 0.6 - - - -
33B ILE* 3.8 17.0 - - + -
34B PHE* 1.3 74.0 - - - +
36B ARG* 1.3 64.0 + - - +
37B CYS* 3.7 3.6 + - + -
52B GLY 3.5 0.7 - - - +
53B ASP* 3.4 1.2 - - - -
54B ARG 3.1 31.2 + - - +
56B ILE* 4.5 5.4 - - + +
109B LEU* 3.9 21.5 - - + -
111B GLU 3.1 15.7 - - - +
112B VAL* 3.9 4.7 - - - -
113B TYR* 3.7 10.8 - - - -
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Residues in contact with ARG 36 (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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35B ALA* 1.3 71.9 - - - +
37B CYS* 1.3 60.0 + - - +
51B SER* 4.7 2.7 - - - +
52B GLY* 3.2 13.5 - - - +
53B ASP* 3.2 17.9 - - - +
109B LEU* 4.0 1.0 - - - -
110B GLU* 3.0 59.1 + - + +
111B GLU* 2.8 61.3 + - + +
113B TYR* 3.6 11.7 + - - +
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Residues in contact with CYS 37 (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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35B ALA 4.1 8.5 - - - +
36B ARG* 1.3 75.8 - - - +
38B LYS* 1.3 64.4 + - - +
39B VAL* 4.4 11.0 - - - -
51B SER* 3.1 3.1 - - - -
52B GLY 2.8 18.8 + - - +
54B ARG* 2.8 59.0 + - - -
56B ILE* 4.2 13.7 - - - -
66B ILE* 4.8 1.6 - - - -
107B VAL* 4.0 12.3 - - + -
108B GLU 3.2 15.5 - - - +
109B LEU* 4.6 5.8 - - + -
110B GLU* 4.3 2.9 - - - -
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Residues in contact with LYS 38 (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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37B CYS* 1.3 75.0 - - - +
39B VAL* 1.3 62.1 + - - +
40B HIS* 4.3 19.7 - - + +
48B GLU* 5.8 0.2 - - - +
49B LEU 3.5 8.5 - - - +
50B GLY* 4.2 3.6 - - - -
51B SER* 3.7 26.2 - - - +
106B GLU 3.9 0.2 - - - +
107B VAL* 3.7 2.3 - - - -
108B GLU* 2.8 49.1 + - + +
110B GLU* 3.0 28.0 + - - +
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Residues in contact with VAL 39 (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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37B CYS* 4.4 11.4 - - - -
38B LYS* 1.3 78.1 - - - +
40B HIS* 1.3 65.1 + - - +
41B TYR 4.3 0.4 - - - -
47B SER* 4.2 0.6 + - - +
48B GLU* 3.6 9.2 - - - +
49B LEU* 3.0 55.0 + - + -
54B ARG* 4.5 0.4 - - - +
66B ILE* 4.3 18.2 - - + -
76B ASN* 3.5 26.2 - - + +
105B LEU* 3.6 22.4 - - + -
106B GLU 3.3 10.3 - - - +
107B VAL* 4.1 11.4 - - + -
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Residues in contact with HIS 40 (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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38B LYS* 4.3 19.6 - - + +
39B VAL* 1.3 77.0 - - - +
41B TYR* 1.3 61.1 + - - +
42B ASP 4.3 0.2 - - - -
47B SER 3.9 0.2 - - - -
48B GLU* 2.6 39.8 + - - +
93B VAL* 6.2 0.4 - - + -
104B THR* 3.8 2.6 - - - +
105B LEU* 3.5 3.0 - - - +
106B GLU* 2.6 76.0 + - + +
108B GLU* 3.9 23.9 + - + -
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Residues in contact with TYR 41 (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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128A LEU* 5.4 3.8 - - + -
39B VAL 4.3 0.2 - - - -
40B HIS* 1.3 74.2 - - - +
42B ASP* 1.3 67.1 + - - +
43B GLY* 3.9 6.3 - - - -
44B ARG* 3.2 15.5 + - - +
45B ALA* 3.0 39.6 + - + +
46B LYS* 3.3 6.9 - - - +
47B SER* 2.9 56.9 + - - +
48B GLU* 4.6 0.4 + - - -
76B ASN* 4.0 15.3 - - - +
77B TRP 4.8 6.5 - - - -
78B GLN* 3.9 18.6 - - - -
103B GLU* 2.2 35.6 + - - -
104B THR 3.5 10.1 - - - -
105B LEU* 4.1 10.5 - - + -
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Residues in contact with ASP 42 (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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239A LYS* 2.9 29.6 + - - -
41B TYR* 1.3 75.3 - - - +
43B GLY* 1.3 53.7 + - - +
45B ALA 3.6 3.1 - - - +
46B LYS* 3.4 31.1 - - + +
103B GLU* 3.4 0.9 - - - +
104B THR* 2.5 50.4 + - + +
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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