Contacts of the helix formed by residues 96 - 118 (chain A) in PDB entry 4X61
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 VAL 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A SER* 2.9 12.6 + - - +
95A LYS* 1.3 76.4 - - - +
97A GLU* 1.3 60.4 + - - +
98A LYS* 3.6 21.1 - - + +
99A ILE* 3.3 19.5 + - + +
100A ARG* 2.9 27.8 + - - +
213B TYR* 3.4 30.7 - - + -
233B GLU* 3.8 29.8 - - + +
234B ASN* 4.0 20.4 - - + +
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Residues in contact with GLU 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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95A LYS 3.6 4.2 + - - -
96A VAL* 1.3 70.5 - - - +
98A LYS* 1.3 67.7 + - + +
100A ARG* 3.0 29.9 + - + +
101A ARG* 2.9 64.1 + - + +
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Residues in contact with LYS 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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55A ILE* 4.9 3.7 - - + +
56A GLN* 3.5 31.5 + - - +
96A VAL* 3.4 13.4 - - + +
97A GLU* 1.3 79.2 - - + +
99A ILE* 1.3 63.8 + - + +
101A ARG* 3.5 6.9 + - - +
102A ASN* 3.1 32.7 + - - +
234B ASN* 5.6 3.6 - - - +
255B SER* 3.3 34.7 + - - +
256B GLN* 4.3 16.1 - - + +
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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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51A LYS* 5.7 9.9 - - - +
89A TRP* 5.1 5.4 - - + +
91A ARG* 4.0 9.0 - - + +
94A SER* 3.6 22.9 - - - +
96A VAL* 3.3 23.9 + - + +
97A GLU 3.2 0.2 - - - -
98A LYS* 1.3 75.6 - - + +
100A ARG* 1.3 58.4 + - - +
102A ASN* 3.9 4.6 - - - +
103A SER* 2.7 47.8 + - - +
233B GLU* 3.4 41.7 - - + +
256B GLN* 6.1 0.4 - - - +
257B CYS* 5.6 4.5 - - + -
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Residues in contact with ARG 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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91A ARG 4.2 7.2 - - - -
92A PRO* 3.0 25.5 - - - +
93A ASP* 4.5 2.5 - - - +
94A SER* 2.9 27.5 + - - +
95A LYS* 3.2 21.2 + - - +
96A VAL 2.9 10.1 + - - +
97A GLU* 3.0 37.9 + - + +
99A ILE* 1.3 79.0 - - - +
101A ARG* 1.3 58.5 + - + +
103A SER* 3.2 2.1 + - - -
104A GLU* 2.9 36.2 + - - +
133A ASN* 3.9 12.8 - - - +
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Residues in contact with ARG 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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55A ILE* 3.7 27.0 - - + +
97A GLU* 2.9 51.6 + - + +
98A LYS* 4.0 3.1 - - - +
100A ARG* 1.3 75.8 - - + +
102A ASN* 1.3 61.8 + - - +
104A GLU* 3.3 18.9 + - - +
105A ALA* 3.2 22.9 + - - +
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Residues in contact with ASN 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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52A ARG 4.3 8.5 - - - +
53A GLU* 2.8 30.6 + - - +
54A PHE* 2.8 42.7 + - + +
55A ILE* 4.1 7.8 + - - +
89A TRP* 5.0 6.3 - - + -
98A LYS* 3.1 24.7 + - - +
99A ILE* 3.9 5.8 - - + +
101A ARG* 1.3 73.7 - - - +
103A SER* 1.3 56.9 - - - +
105A ALA* 3.4 4.3 + - - +
106A ALA* 2.8 35.9 + - - +
256B GLN* 4.2 6.5 + - - -
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Residues in contact with SER 103 (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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89A TRP* 4.2 6.0 + - - -
90A ILE* 3.5 8.8 - - - +
91A ARG 2.9 45.0 + - - -
92A PRO* 3.5 4.9 - - - -
99A ILE* 2.7 28.7 + - - +
100A ARG 3.6 2.5 - - - -
102A ASN* 1.3 72.7 - - - +
104A GLU* 1.3 57.1 + - - +
106A ALA* 3.4 7.1 - - - +
107A MET* 2.6 38.6 + - - +
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Residues in contact with GLU 104 (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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92A PRO* 4.9 3.1 - - + +
100A ARG* 2.9 25.5 + - - +
101A ARG* 3.3 19.5 + - - +
103A SER* 1.3 77.7 - - - +
105A ALA* 1.3 63.4 + - - +
107A MET* 3.2 4.0 + - - +
108A LEU* 3.1 29.1 + - + +
133A ASN* 3.0 31.0 + - - +
136A ARG* 3.7 23.8 + - - +
137A VAL* 4.0 19.0 - - + +
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Residues in contact with ALA 105 (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 PHE* 3.7 34.0 - - + -
101A ARG 3.2 9.1 + - - +
102A ASN 3.7 6.7 - - - +
104A GLU* 1.3 79.5 - - - +
106A ALA* 1.3 58.4 + - - +
108A LEU* 3.4 10.1 + - - +
109A GLN* 3.0 28.8 + - - +
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Residues in contact with ALA 106 (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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52A ARG* 4.7 1.6 - - - +
54A PHE* 3.7 15.0 - - + -
89A TRP* 3.5 31.2 - - + -
90A ILE* 3.8 14.1 - - + -
102A ASN 2.8 21.7 + - - +
103A SER* 3.4 5.4 - - - +
105A ALA* 1.3 73.0 - - - +
107A MET* 1.3 57.5 + - - +
109A GLN* 3.4 3.4 - - - +
110A GLU* 3.0 35.5 + - - +
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Residues in contact with MET 107 (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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86A LEU* 3.9 23.1 - - + +
90A ILE* 4.0 6.9 - - + +
92A PRO* 4.0 10.1 - - - -
103A SER 2.6 19.6 + - - +
104A GLU 3.5 4.7 - - - +
106A ALA* 1.3 70.7 - - - +
108A LEU* 1.3 59.9 + - - +
110A GLU* 3.4 1.4 + - - +
111A LEU* 2.9 43.5 + - + +
124A LEU* 3.6 27.1 - - + -
134A LEU* 3.4 41.7 - - + +
137A VAL* 3.7 20.4 - - + -
138A LEU* 3.6 21.1 - - + +
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Residues in contact with LEU 108 (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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104A GLU* 3.1 21.5 + - + +
105A ALA* 3.7 9.2 - - - +
107A MET* 1.3 76.8 - - - +
109A GLN* 1.3 64.4 + - - +
111A LEU* 3.7 3.2 - - + +
112A ASN* 2.8 40.4 + - - +
136A ARG* 6.4 0.2 - - - +
137A VAL* 3.9 22.2 - - + +
140A ASN* 5.4 3.6 - - + -
141A HIS* 4.2 28.5 - - + +
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Residues in contact with GLN 109 (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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46A PHE* 3.9 15.7 - - + -
52A ARG* 2.8 41.9 + - - +
54A PHE* 3.3 28.7 - - + -
66A GLN* 5.0 11.3 + - - +
105A ALA 3.0 18.3 + - - +
106A ALA 3.4 4.5 - - - +
108A LEU* 1.3 76.0 - - - +
110A GLU* 1.3 56.7 + - - +
112A ASN* 3.3 7.0 + - - +
113A PHE* 2.9 28.9 + - + +
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Residues in contact with GLU 110 (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 VAL* 4.4 4.8 - - + +
46A PHE* 3.7 28.5 - - + +
52A ARG* 3.0 25.5 + - - +
85A LYS 3.9 3.2 - - - +
86A LEU* 3.4 13.2 - - + +
87A SER* 2.7 47.5 + - - -
90A ILE* 3.4 13.2 - - - +
106A ALA 3.0 20.5 + - - +
107A MET 3.9 2.5 - - - +
109A GLN* 1.3 75.3 - - - +
111A LEU* 1.3 63.3 + - - +
113A PHE* 3.1 4.0 + - - +
114A GLY 3.0 18.2 + - - -
122A PHE* 3.8 17.6 - - + -
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Residues in contact with LEU 111 (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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86A LEU* 5.1 0.7 - - + -
107A MET* 2.9 50.4 + - + +
108A LEU* 3.7 4.3 - - + +
110A GLU* 1.3 75.4 - - - +
112A ASN* 1.3 58.0 + - - +
114A GLY* 3.1 4.0 + - - -
115A ALA* 3.0 27.2 + - - +
122A PHE* 3.8 35.0 - - + -
124A LEU* 4.5 8.3 - - + -
137A VAL 4.9 1.1 - - - +
138A LEU* 4.1 7.6 - - + -
141A HIS* 3.6 43.5 + - + +
151A PHE* 3.8 22.7 - - + -
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Residues in contact with ASN 112 (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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108A LEU* 2.8 38.8 + - - +
109A GLN* 3.6 6.1 - - - +
111A LEU* 1.3 71.6 - - - +
113A PHE* 1.3 52.0 + - - +
115A ALA* 3.2 7.7 + - - +
116A TYR* 2.7 35.7 + - - +
141A HIS* 3.4 20.9 + - - -
144A THR* 5.6 5.4 - - - +
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Residues in contact with PHE 113 (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 VAL* 4.3 13.5 - - + -
46A PHE* 3.9 26.7 - + + -
67A THR* 3.7 25.8 - - + -
68A ARG* 4.0 11.0 - - + -
70A ASP* 5.1 5.6 - - - -
78A TRP* 6.1 0.4 - + - -
109A GLN* 2.9 14.6 + - + +
110A GLU 3.1 8.5 + - - +
112A ASN* 1.3 73.1 - - - +
114A GLY* 1.3 61.2 + - - +
116A TYR* 3.4 30.4 - + + +
117A LEU* 2.9 58.7 + - + +
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Residues in contact with GLY 114 (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 VAL* 5.3 1.5 - - - +
110A GLU 3.0 13.5 + - - -
111A LEU 3.1 4.2 + - - -
113A PHE* 1.3 76.5 - - - +
115A ALA* 1.3 55.0 + - - +
117A LEU* 3.2 3.4 + - - +
118A GLY 2.9 23.6 + - - -
119A LEU* 3.2 36.1 + - - -
122A PHE* 4.4 10.8 - - - -
149A SER* 5.7 2.2 - - - -
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Residues in contact with ALA 115 (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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111A LEU 3.0 11.9 + - - +
112A ASN* 3.5 12.3 - - - +
114A GLY* 1.3 75.2 - - - +
116A TYR* 1.3 64.4 + - - +
118A GLY* 3.1 14.7 + - - +
119A LEU 5.3 0.2 - - - +
141A HIS* 4.5 6.7 - - + +
147A HIS* 4.2 34.2 - - + +
149A SER* 5.5 9.6 + - - -
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Residues in contact with TYR 116 (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 ASP* 2.7 37.0 + - + -
112A ASN 2.7 21.1 + - - +
113A PHE* 3.4 35.9 - + + +
115A ALA* 1.3 74.1 - - - +
117A LEU* 1.3 65.3 + - + +
118A GLY* 3.4 1.0 + - - -
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Residues in contact with LEU 117 (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 VAL* 4.5 12.8 - - + -
70A ASP* 3.6 26.5 - - + -
75A GLY* 5.9 0.7 - - - -
78A TRP* 3.4 72.3 - - + +
79A ASN* 3.9 3.5 + - - -
113A PHE* 2.9 48.6 + - + +
114A GLY 3.6 4.7 - - - +
116A TYR* 1.3 78.3 - - + +
118A GLY* 1.3 60.8 + - - +
119A LEU* 4.0 15.5 - - + -
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Residues in contact with GLY 118 (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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78A TRP 4.3 0.7 - - - -
79A ASN* 2.8 29.3 + - - +
114A GLY 2.9 4.6 + - - -
115A ALA* 3.1 15.3 + - - -
116A TYR 3.2 0.6 - - - -
117A LEU* 1.3 78.8 - - - +
119A LEU* 1.3 67.2 + - - +
120A PRO* 3.5 2.4 - - - +
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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