Contacts of the strand formed by residues 30 - 42 (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 MET 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ALA* 4.8 1.1 - - - -
29A ALA* 1.3 77.8 - - - +
31A LEU* 1.3 63.8 + - - +
32A THR* 4.3 2.9 + - - +
57A ILE* 5.3 7.0 - - + -
58A VAL 3.8 5.2 - - - +
59A LYS* 4.7 10.5 - - - -
60A PRO* 4.1 12.1 - - + -
116A SER 3.5 3.6 - - - +
117A VAL* 3.6 1.7 - - - -
118A PHE* 3.0 49.2 + - + +
120A ALA* 3.5 28.9 - - + +
53B ASP 4.6 0.2 - - - +
54B ARG* 4.5 2.7 - - - -
55B VAL* 3.7 32.5 - - + +
67B HIS* 4.0 15.3 - - - +
68B GLN 3.9 6.5 - - - +
69B SER* 3.9 26.7 - - - +
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Residues in contact with LEU 31 (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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21A VAL* 3.7 38.1 - - + +
24A ALA* 3.9 23.6 - - + -
25A LEU* 5.5 4.9 - - + -
29A ALA 3.8 1.2 + - - -
30A MET* 1.3 73.4 - - - +
32A THR* 1.3 63.4 + - - +
33A ILE* 4.1 17.0 - - + -
56A ILE 4.4 0.2 - - - -
57A ILE* 3.3 8.8 - - - +
58A VAL* 3.0 58.0 + - + +
84A VAL* 6.4 0.2 - - + -
94A LEU* 4.9 5.2 - - + -
115A VAL* 4.1 20.6 - - + -
116A SER 3.5 15.3 - - - +
117A VAL* 4.3 4.0 - - + -
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Residues in contact with THR 32 (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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30A MET* 4.3 7.4 + - - +
31A LEU* 1.3 76.6 + - - +
33A ILE* 1.3 66.8 + - - +
34A PHE* 4.0 23.3 - - + -
55A VAL* 4.3 5.4 - - + -
56A ILE 3.4 7.2 - - - +
57A ILE* 4.2 15.4 - - + +
114A MET* 4.1 2.2 - - + +
115A VAL* 3.5 1.0 - - - -
116A SER* 2.9 50.8 + - - +
118A PHE* 5.2 0.2 - - - +
32B THR* 4.7 3.4 - - + -
34B PHE* 3.4 29.2 - - + -
55B VAL* 4.9 5.5 - - - +
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Residues in contact with ILE 33 (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* 4.4 13.9 - - + -
21A VAL* 4.4 3.1 - - + -
31A LEU* 4.1 19.7 - - + -
32A THR* 1.3 80.2 - - - +
34A PHE* 1.3 69.7 + - - +
35A ALA* 3.6 25.8 - - + -
54A ARG 3.6 0.9 - - - +
55A VAL* 3.5 0.9 - - - -
56A ILE* 2.8 52.2 + - + +
94A LEU* 3.8 27.6 - - + -
109A LEU* 4.4 13.2 - - + -
112A VAL* 4.2 8.3 - - + -
114A MET 3.4 8.1 - - - +
115A VAL* 4.0 14.8 - - + -
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Residues in contact with PHE 34 (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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32A THR* 4.0 9.9 - - + -
33A ILE* 1.3 78.0 - - - +
35A ALA* 1.3 61.7 + - - +
54A ARG 3.6 3.4 - - - -
55A VAL* 3.8 27.6 - - + -
112A VAL 3.7 0.2 - - - -
113A TYR* 2.8 27.9 + - + -
114A MET* 2.9 55.4 + - + +
6B VAL* 4.0 11.0 - - + -
32B THR* 3.2 35.9 - - + -
114B MET* 5.8 0.2 - - + -
116B SER* 3.7 17.5 - - - -
118B PHE* 3.7 40.4 - + + -
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Residues in contact with ALA 35 (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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33A ILE* 3.6 18.8 - - + -
34A PHE* 1.3 77.4 - - - +
36A ARG* 1.3 67.7 + - - +
37A CYS* 3.7 3.6 + - - -
52A GLY 3.5 0.9 - - - +
53A ASP* 3.4 0.2 - - - -
54A ARG* 2.9 34.1 + - - +
56A ILE* 4.6 4.5 - - + +
109A LEU* 4.0 16.8 - - + -
111A GLU 3.3 13.5 - - - +
112A VAL* 3.9 6.3 - - + -
113A TYR* 3.6 9.3 - - - -
118B PHE* 4.1 0.6 - - - -
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Residues in contact with ARG 36 (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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35A ALA* 1.3 74.0 - - - +
37A CYS* 1.3 62.6 + - - +
51A SER* 3.3 17.8 + - - +
52A GLY* 3.3 10.3 - - - +
53A ASP* 3.4 7.6 - - - +
109A LEU 3.8 0.7 - - - -
110A GLU* 2.9 59.3 + - - +
111A GLU* 2.8 44.0 + - + +
113A TYR* 3.1 27.0 - - + +
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Residues in contact with CYS 37 (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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35A ALA 4.0 6.7 - - - +
36A ARG* 1.3 77.8 - - - +
38A LYS* 1.3 59.1 + - - +
39A VAL* 4.3 4.9 - - - -
51A SER* 3.2 2.6 - - - -
52A GLY 2.8 19.4 + - - -
54A ARG* 2.8 52.5 + - - -
56A ILE* 4.1 11.2 - - - -
66A ILE* 5.2 0.4 - - - -
107A VAL* 3.8 25.1 - - + -
108A GLU 3.1 17.5 - - - +
109A LEU* 4.3 6.5 - - + -
110A GLU* 3.9 6.3 - - - -
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Residues in contact with LYS 38 (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* 1.3 72.6 - - - +
39A VAL* 1.3 65.5 + - - +
40A HIS* 4.0 21.8 - - + +
49A LEU 3.5 9.4 - - - +
50A GLY* 4.6 2.5 - - - -
51A SER* 3.7 28.0 - - - +
54A ARG* 4.3 0.2 - - - +
106A GLU 3.7 0.9 - - - +
107A VAL* 3.5 3.5 - - - +
108A GLU* 2.9 54.7 + - + +
110A GLU* 3.6 22.6 + - - +
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Residues in contact with VAL 39 (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* 4.3 7.6 - - - -
38A LYS* 1.3 79.4 - - - +
40A HIS* 1.3 68.0 + - - +
47A SER 4.2 0.5 - - - +
48A GLU* 3.5 5.4 - - - -
49A LEU* 3.0 53.0 + - + -
54A ARG* 4.4 0.7 - - - +
66A ILE* 3.7 34.1 - - + -
76A ASN* 3.4 32.4 - - - +
105A LEU* 3.7 13.5 - - + -
106A GLU 3.5 4.7 - - - +
107A VAL* 4.1 10.3 - - + -
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Residues in contact with HIS 40 (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* 4.0 29.0 - - + +
39A VAL* 1.3 74.9 + - - +
41A TYR* 1.3 60.0 + - - +
47A SER 4.0 0.4 - - - -
48A GLU* 2.4 44.2 + - - +
49A LEU 5.3 0.4 - - - -
93A VAL* 6.2 0.2 - - + -
104A THR* 3.8 2.2 - - - +
105A LEU* 3.6 3.4 - - - +
106A GLU* 2.8 66.9 + - + +
108A GLU* 3.9 22.6 + - + +
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Residues in contact with TYR 41 (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* 1.3 75.4 - - - +
42A ASP* 1.3 72.1 + - - +
43A GLY* 4.0 0.7 - - - -
44A ARG* 3.2 7.6 + - - +
45A ALA* 3.2 44.8 + - + +
46A LYS* 3.2 8.5 - - - +
47A SER* 2.9 62.2 + - - +
48A GLU* 4.6 0.2 + - - -
76A ASN* 3.9 9.9 - - - +
77A TRP 5.2 6.7 - - - -
78A GLN* 5.2 4.5 - - - -
103A GLU* 2.5 36.4 + - + -
104A THR 3.4 12.3 - - - -
105A LEU* 3.8 19.5 - - + -
128B LEU* 5.5 4.0 - - + -
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Residues in contact with ASP 42 (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 4.4 0.2 - - - -
41A TYR* 1.3 77.0 - - - +
43A GLY* 1.3 61.1 + - - +
45A ALA 3.6 3.0 - - - +
46A LYS* 3.6 24.2 - - + +
103A GLU* 3.4 0.7 - - - -
104A THR* 2.6 48.8 + - + +
239B LYS* 3.4 18.7 + - - +
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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