Contacts of the helix formed by residues 79 - 102 (chain A) in PDB entry 2K1S
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 GLY 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A SER 3.5 1.8 + - - -
78A GLY* 1.3 80.9 - - - +
80A HIS* 1.3 54.5 + - - +
81A ASP 3.0 3.6 - - - -
82A LEU* 2.8 20.4 + - - +
83A ASN* 2.8 41.4 + - - +
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Residues in contact with HIS 80 (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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76A SER* 3.8 31.2 + - - +
79A GLY* 1.3 72.0 - - - +
81A ASP* 1.3 82.9 + - - +
83A ASN* 3.9 2.5 - - - +
84A MET* 3.0 34.7 + - + +
115A PRO* 4.4 11.1 - - + +
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Residues in contact with ASP 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLY 3.0 0.8 - - - -
80A HIS* 1.3 110.7 + - - +
82A LEU* 1.3 64.1 + - + +
84A MET* 3.1 10.2 + - - +
85A ARG* 3.0 32.4 + - + +
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLY 5.1 4.7 - - - +
79A GLY* 2.8 18.0 + - - +
81A ASP* 1.3 79.1 - - + +
83A ASN* 1.3 64.0 + - - +
85A ARG* 3.2 33.7 + - - +
86A LEU* 3.1 21.0 + - - +
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Residues in contact with ASN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR* 3.6 17.1 + - + +
75A ASP 3.0 28.6 + - - +
76A SER* 3.6 14.4 - - - +
77A THR 4.2 5.9 + - - +
78A GLY* 4.2 1.6 + - - -
79A GLY 2.8 40.7 + - - +
80A HIS 4.0 4.9 - - - +
82A LEU* 1.3 74.2 - - - +
84A MET* 1.3 54.3 + - - +
86A LEU* 3.3 13.1 + - - +
87A SER* 2.8 35.4 + - - -
115A PRO* 5.4 2.2 - - + -
132A ARG* 5.1 6.9 - - - +
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Residues in contact with MET 84 (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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80A HIS* 3.0 22.9 + - + +
81A ASP* 3.2 14.8 - - - +
83A ASN* 1.3 74.7 - - - +
85A ARG* 1.3 65.0 + - + +
87A SER* 3.3 4.5 + - - -
88A GLN* 3.0 25.1 + - - +
112A GLY* 3.4 31.4 - - - +
113A LEU* 4.8 4.7 - - + -
114A GLY 4.6 1.1 - - - +
115A PRO* 3.7 33.8 - - + +
116A ALA* 5.6 2.7 - - + -
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Residues in contact with ARG 85 (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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81A ASP 3.0 14.5 + - - +
82A LEU* 3.3 35.6 + - - +
84A MET* 1.3 76.9 - - + +
86A LEU* 1.3 53.0 + - - +
88A GLN* 3.2 5.6 + - - +
89A GLN* 2.7 46.9 + - - +
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Residues in contact with LEU 86 (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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41A SER* 3.5 23.6 - - - +
42A SER* 3.9 7.0 - - - -
43A ALA 4.0 1.6 - - - +
74A THR* 5.1 10.5 - - + +
82A LEU 3.1 9.4 + - - +
83A ASN* 3.7 16.4 - - - +
85A ARG* 1.3 75.9 - - - +
87A SER* 1.3 60.1 + - - +
89A GLN* 3.3 27.3 - - - +
90A ARG* 2.9 68.1 + - + +
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Residues in contact with SER 87 (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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72A GLY* 2.7 34.9 + - - -
73A TYR 5.7 0.7 - - - -
74A THR* 4.0 16.5 - - - +
83A ASN 2.8 18.6 + - - -
84A MET* 3.3 9.9 - - - -
85A ARG 3.2 0.2 - - - -
86A LEU* 1.3 77.4 - - - +
88A GLN* 1.3 61.4 + - - +
90A ARG* 3.5 7.8 + - - +
91A ALA* 3.2 21.1 + - - +
112A GLY* 3.1 15.6 - - - -
114A GLY* 3.4 7.5 + - - -
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Residues in contact with GLN 88 (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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84A MET 3.0 15.6 + - - +
85A ARG* 3.8 4.5 - - - +
87A SER* 1.3 74.0 + - - +
89A GLN* 1.3 60.6 + - - +
91A ALA* 3.2 3.9 + - - +
92A ASP* 2.8 34.9 + - + +
110A THR* 2.9 42.7 + - - +
111A GLN* 3.6 1.3 - - - -
112A GLY* 2.8 35.1 + - - -
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Residues in contact with GLN 89 (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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42A SER* 3.9 6.0 - - - -
43A ALA* 3.0 37.4 + - + +
85A ARG* 2.7 32.8 + - - +
86A LEU* 3.3 19.7 - - - +
88A GLN* 1.3 72.9 - - - +
90A ARG* 1.3 57.7 + - - +
92A ASP* 3.2 7.9 + - - +
93A SER* 2.9 32.8 + - - +
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Residues in contact with ARG 90 (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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34A ASN* 2.7 45.5 + - - +
38A PHE* 3.5 31.6 - - + -
41A SER* 2.7 33.5 + - - +
43A ALA* 3.9 17.5 - - + -
72A GLY* 5.7 0.7 - - - -
73A TYR 4.9 4.1 + - - -
74A THR* 5.3 4.7 + - - -
86A LEU* 2.9 45.1 + - + +
87A SER* 3.8 6.3 - - - +
89A GLN* 1.3 75.4 - - - +
91A ALA* 1.3 62.6 + - - +
93A SER* 3.3 3.6 + - - -
94A VAL* 3.2 26.8 + - - +
132A ARG* 4.4 20.6 - - - +
133A ARG* 4.4 5.2 - - - +
134A VAL* 4.1 13.8 - - + +
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Residues in contact with ALA 91 (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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70A VAL* 3.4 38.4 - - + +
72A GLY* 4.4 7.8 - - - +
87A SER 3.2 11.4 + - - +
88A GLN* 3.2 11.3 + - - +
90A ARG* 1.3 79.2 - - - +
92A ASP* 1.3 57.4 + - - +
94A VAL* 3.2 5.6 + - - +
95A ALA 3.0 23.4 + - - -
110A THR* 3.4 19.5 - - - +
111A GLN 4.5 3.1 - - - +
134A VAL* 5.1 2.0 - - - +
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Residues in contact with ASP 92 (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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88A GLN* 2.8 24.0 + - + +
89A GLN* 3.5 7.6 - - - +
91A ALA* 1.3 74.9 - - - +
93A SER* 1.3 55.9 + - - +
95A ALA* 4.3 2.5 - - - +
96A SER* 2.8 45.1 + - - -
110A THR* 3.9 13.5 + - + +
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Residues in contact with SER 93 (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 PHE* 4.4 1.3 - - - -
43A ALA* 3.1 25.1 + - - +
45A LEU* 3.8 29.1 - - - +
89A GLN* 2.9 17.1 + - - +
90A ARG 3.5 8.7 - - - -
92A ASP* 1.3 77.9 + - - +
94A VAL* 1.3 62.2 + - - +
96A SER* 3.1 16.9 + - - -
97A ALA* 3.2 15.2 + - - +
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Residues in contact with VAL 94 (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 MET* 5.8 0.7 - - - -
37A THR* 4.8 6.7 - - + -
38A PHE* 4.6 10.5 - - + -
45A LEU* 5.4 0.4 - - + -
53A LEU* 3.9 25.5 - - + +
70A VAL* 3.8 10.8 - - + -
90A ARG 3.3 14.8 - - - +
91A ALA 3.2 7.1 + - - +
93A SER* 1.3 76.5 - - - +
95A ALA* 1.3 63.4 + - - +
97A ALA* 3.3 7.3 + - - +
98A LEU* 3.0 37.7 + - + +
134A VAL* 4.1 20.2 - - + -
136A ILE* 3.9 27.1 - - + -
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Residues in contact with ALA 95 (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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70A VAL* 4.6 2.0 - - + +
91A ALA 3.0 6.9 + - - +
92A ASP* 3.7 6.1 - - - +
94A VAL* 1.3 76.7 - - - +
96A SER* 1.3 57.5 + - - +
98A LEU* 3.0 9.7 + - - +
99A ILE* 2.9 38.3 + - + +
108A ILE* 3.7 22.2 - - + -
110A THR* 3.4 31.6 - - + -
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Residues in contact with SER 96 (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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45A LEU* 5.6 0.5 - - - +
92A ASP* 2.8 32.3 + - - -
93A SER* 3.1 15.8 + - - -
95A ALA* 1.3 73.9 - - - +
97A ALA* 1.3 52.3 + - - +
99A ILE* 3.4 12.2 + - - +
100A THR* 2.7 40.4 + - - -
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Residues in contact with ALA 97 (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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45A LEU* 4.0 18.6 - - + +
50A ALA* 6.3 1.1 - - + -
53A LEU* 4.0 19.3 - - + -
93A SER 3.2 19.7 + - - +
94A VAL 3.5 5.2 - - - +
96A SER* 1.3 77.6 + - - +
98A LEU* 1.3 56.8 + - - +
100A THR* 3.4 7.4 + - - +
101A GLN* 3.0 29.3 + - - +
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Residues in contact with LEU 98 (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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53A LEU* 3.7 30.1 - - + +
56A VAL* 4.6 8.5 - - + -
57A ALA* 3.9 15.9 - - + +
60A LEU* 3.9 11.2 - - + -
68A VAL* 3.8 29.6 - - + -
70A VAL* 4.7 0.9 - - + -
94A VAL* 3.0 38.3 + - + +
95A ALA* 3.0 7.8 + - - +
97A ALA* 1.3 73.9 - - - +
99A ILE* 1.3 65.3 + - - +
101A GLN* 3.0 5.8 + - - -
102A GLY 2.9 8.3 + - - -
103A VAL* 2.9 31.2 + - + +
108A ILE* 3.8 10.5 - - + -
136A ILE* 5.4 1.6 - - + -
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Residues in contact with ILE 99 (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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95A ALA* 2.9 30.6 + - + +
96A SER* 3.8 8.7 - - - +
98A LEU* 1.3 73.7 - - - +
100A THR* 1.3 63.8 + - - +
102A GLY* 3.2 13.5 + - - -
103A VAL 3.2 18.0 + - - +
105A ALA* 3.7 31.9 - - + +
108A ILE* 3.7 17.7 - - + -
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Residues in contact with THR 100 (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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96A SER* 2.7 25.3 + - - -
97A ALA* 3.4 8.9 - - - +
99A ILE* 1.3 78.7 - - - +
101A GLN* 1.3 63.2 + - - +
102A GLY* 3.5 0.7 + - - -
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Residues in contact with GLN 101 (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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54A THR* 3.1 42.4 + - + +
57A ALA* 3.8 25.6 - - + -
58A MET* 5.6 2.0 - - + +
61A LYS* 2.8 28.7 + - - +
97A ALA 3.0 16.6 + - - +
98A LEU 3.0 4.7 + - - +
100A THR* 1.3 79.1 - - - +
102A GLY* 1.3 58.0 + - - +
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Residues in contact with GLY 102 (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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61A LYS* 3.6 23.1 - - - +
98A LEU 2.9 1.0 + - - -
99A ILE 3.2 8.4 + - - -
100A THR 4.4 0.9 - - - -
101A GLN* 1.3 81.4 - - - +
103A VAL* 1.3 64.6 + - - +
104A ASP* 3.8 5.0 + - - +
107A ARG* 5.7 0.2 + - - -
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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