Contacts of the strand formed by residues 46 - 58 (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 LYS 46 (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* 3.2 12.8 - - - +
42A ASP* 3.6 24.2 - - - +
45A ALA* 1.3 77.7 - - - +
47A SER* 1.3 66.2 + - - +
48A GLU* 5.1 14.3 + - - +
128B LEU* 3.2 5.0 - - - +
129B THR* 2.7 54.7 + - + +
239B LYS* 4.2 17.0 - - + +
240B ARG* 4.8 22.1 - - - +
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL 4.9 0.9 + - - -
41A TYR* 2.9 41.5 + - - +
46A LYS* 1.3 80.1 - - - +
48A GLU* 1.3 73.0 + - - +
76A ASN* 3.1 26.0 + - - -
126B LEU* 3.7 16.2 - - - +
127B ALA 3.1 12.3 - - - -
128B LEU* 4.2 11.2 - - - -
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL 3.5 4.0 - - - +
40A HIS* 2.4 51.2 + - - +
46A LYS* 5.1 14.6 + - - +
47A SER* 1.3 79.4 - - - +
49A LEU* 1.3 62.9 + - - +
50A GLY 4.3 0.2 - - - -
125B GLU 4.5 0.9 - - - +
126B LEU* 3.6 3.5 - - - +
127B ALA* 2.9 40.4 + - + +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 3.5 5.2 - - - +
39A VAL* 3.0 47.0 + - + +
40A HIS* 5.3 0.2 - - - -
48A GLU* 1.3 78.8 + - - +
50A GLY* 1.3 66.0 + - - +
54A ARG* 3.6 32.3 - - - +
68A GLN* 3.9 5.8 - - - +
75A VAL* 3.7 34.8 - - + -
76A ASN* 4.2 1.1 - - - +
124B GLU 3.9 14.6 - - - +
125B GLU 3.6 30.7 - - - +
126B LEU* 3.8 12.1 - - + +
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Residues in contact with GLY 50 (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 4.0 0.9 - - - -
38A LYS* 4.1 5.8 - - - -
48A GLU 4.3 0.2 - - - -
49A LEU* 1.3 77.3 - - - +
51A SER* 1.3 57.9 + - - -
54A ARG* 2.6 38.3 + - - -
124B GLU* 3.8 26.1 + - - +
125B GLU 5.1 0.6 + - - -
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Residues in contact with SER 51 (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* 3.3 17.8 + - - +
37A CYS 3.2 9.0 - - - -
38A LYS* 3.7 14.8 - - - +
50A GLY* 1.3 71.3 - - - +
52A GLY* 1.3 58.8 + - - +
54A ARG* 3.9 0.2 + - - -
110A GLU* 2.7 31.3 + - - -
122B ASP* 4.4 0.5 - - - +
123B TYR 5.2 1.9 + - - -
124B GLU* 3.7 16.5 + - - +
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Residues in contact with GLY 52 (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 3.5 1.0 - - - +
36A ARG* 3.3 4.8 - - - +
37A CYS 2.8 31.4 + - - +
50A GLY 3.3 1.2 + - - -
51A SER* 1.3 77.5 + - - +
53A ASP* 1.3 66.8 + - - -
54A ARG* 3.3 21.2 + - - -
121B GLU 4.1 5.4 - - - -
122B ASP* 3.6 7.2 - - - -
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Residues in contact with ASP 53 (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 3.4 2.7 - - - -
36A ARG* 3.4 9.4 - - - +
52A GLY* 1.3 70.5 - - - -
54A ARG* 1.3 67.4 + - - +
67A HIS 4.7 0.5 - - - +
68A GLN* 4.7 3.5 - - - -
69A SER* 5.1 1.2 + - - -
113A TYR* 2.7 35.8 + - - -
5B LYS* 3.1 24.3 + - - +
118B PHE* 3.8 6.7 - - + -
120B ALA* 3.6 16.4 - - + +
121B GLU* 2.9 46.4 + - - +
122B ASP* 3.7 12.7 - - - +
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Residues in contact with ARG 54 (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 0.5 - - - +
34A PHE* 3.6 1.2 - - - -
35A ALA 2.9 31.9 + - - +
37A CYS* 2.8 49.5 + - - -
38A LYS* 4.3 1.2 - - - +
39A VAL* 4.4 1.2 - - - +
49A LEU* 3.6 38.9 + - - +
50A GLY 2.6 23.6 + - - -
51A SER 3.7 0.6 + - - -
52A GLY* 3.3 14.9 + - - -
53A ASP* 1.3 76.0 - - - +
55A VAL* 1.3 61.9 + - - +
56A ILE* 3.9 4.0 + - + +
66A ILE* 4.1 16.6 - - + -
67A HIS 3.1 19.3 - - - +
68A GLN* 4.0 8.5 - - + +
30B MET* 5.8 0.7 - - - -
118B PHE* 3.5 10.6 - - - -
120B ALA* 5.5 0.4 - - - -
122B ASP* 2.7 40.1 + - - +
124B GLU* 3.9 2.0 - - - +
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Residues in contact with VAL 55 (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* 4.3 12.1 - - + -
33A ILE 3.5 3.1 - - - +
34A PHE* 3.8 23.8 - - + -
54A ARG* 1.3 73.5 - - - +
56A ILE* 1.3 62.7 + - - +
57A ILE* 4.2 6.2 + - + +
65A LEU 3.9 0.7 - - - +
66A ILE* 3.6 1.9 - - - -
67A HIS* 2.8 44.0 + - + +
30B MET* 3.8 24.5 - - + -
32B THR* 4.7 7.0 - - + +
57B ILE* 4.3 22.0 - - + -
118B PHE* 3.7 25.8 - - + -
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Residues in contact with ILE 56 (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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31A LEU 3.7 0.3 - - - +
32A THR* 3.4 4.9 - - - +
33A ILE* 2.8 51.9 + - + +
35A ALA* 4.6 4.0 - - + -
37A CYS* 4.1 12.6 - - - -
54A ARG 4.2 6.1 - - - +
55A VAL* 1.3 80.0 - - - +
57A ILE* 1.3 70.0 + - - +
58A VAL* 4.9 1.6 - - + -
64A PHE* 4.0 20.4 - - + -
65A LEU 3.3 7.6 - - - +
66A ILE* 4.5 11.7 - - + -
94A LEU* 4.1 17.7 - - + -
107A VAL* 3.7 28.0 - - + -
109A LEU* 3.8 19.1 - - + -
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Residues in contact with ILE 57 (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* 5.3 9.2 - - + -
31A LEU 3.3 8.1 - - - +
32A THR* 4.2 16.4 - - + +
55A VAL* 4.4 5.6 - - + -
56A ILE* 1.3 80.4 - - - +
58A VAL* 1.3 76.9 + - - +
59A LYS* 4.2 17.3 - - + -
63A SER 3.8 0.3 - - - +
64A PHE* 3.4 4.0 - - - -
65A LEU* 2.6 63.4 + - + +
67A HIS* 5.4 3.6 - - + -
55B VAL* 4.2 19.1 - - + -
57B ILE* 3.9 27.8 - - + -
67B HIS* 4.8 8.7 - - + -
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Residues in contact with VAL 58 (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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25A LEU* 4.3 20.6 - - + -
29A ALA 4.1 1.4 - - - +
30A MET* 3.8 2.8 - - - -
31A LEU* 3.0 55.1 + - + +
56A ILE* 4.9 2.0 - - + -
57A ILE* 1.3 80.6 - - - +
59A LYS* 1.3 71.5 + - - +
60A PRO 4.0 0.2 - - - -
62A GLY* 5.2 1.3 - - - -
63A SER 3.3 6.5 - - - +
64A PHE* 3.9 29.2 - - + -
84A VAL* 4.1 26.0 - - + -
94A LEU* 4.8 6.3 - - + -
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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