Contacts of the helix formed by residues 91 - 112 (chain A) in PDB entry 1ZY3
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 ASN 91 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLY* 2.8 12.7 + - - +
90A PRO* 1.3 78.6 - - - +
92A TRP* 1.3 103.4 + - - +
93A GLY 3.1 0.4 - - - +
94A ARG* 2.8 39.5 + - - +
95A LEU* 3.3 6.2 + - - +
214B ASP* 2.7 28.1 + - - -
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Residues in contact with TRP 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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90A PRO 4.0 0.2 + - - -
91A ASN* 1.3 97.3 + - - +
93A GLY* 1.3 80.0 + - - +
95A LEU* 3.2 10.9 + - - +
96A VAL* 3.0 29.4 + - + +
146A PHE* 5.3 1.9 - - + -
149A LEU* 3.7 49.1 - - + +
156A GLU* 5.1 7.0 - - + -
214B ASP* 3.5 32.8 - - + -
217B ASP* 4.5 10.8 - - - -
218B ARG* 3.5 37.5 - - + -
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Residues in contact with GLY 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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91A ASN 3.1 1.2 - - - -
92A TRP* 1.3 90.3 - - - +
94A ARG* 1.3 67.6 + - - +
96A VAL* 3.8 8.6 - - - +
97A ALA* 2.9 30.0 + - - +
213B GLY 5.8 1.1 - - - -
214B ASP* 3.1 20.3 + - - -
217B ASP* 5.9 2.7 - - - -
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Residues in contact with ARG 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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82A SER* 3.9 12.4 - - - +
85A LEU* 3.7 24.9 - - - +
86A PHE* 3.4 33.6 - - + +
89A GLY 3.4 22.1 + - - +
91A ASN* 2.8 26.9 + - - +
93A GLY* 1.3 91.0 + - - +
95A LEU* 1.3 59.5 + - - +
97A ALA* 3.4 9.3 + - + +
98A PHE* 2.9 31.9 + - - +
209B LEU* 4.5 4.4 + - - +
210B ALA* 3.0 36.8 + - - +
213B GLY* 4.9 1.2 - - - -
214B ASP* 2.6 44.3 + - - +
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Residues in contact with LEU 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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86A PHE* 3.7 22.3 - - + -
90A PRO 5.9 0.2 - - - +
91A ASN 3.3 5.6 + - - +
92A TRP* 3.2 12.7 + - - +
94A ARG* 1.3 80.1 - - - +
96A VAL* 1.3 61.3 + - - +
98A PHE* 3.5 4.4 + - + +
99A PHE* 3.1 23.0 + - - +
129A LEU* 5.3 9.4 - - + -
133A LEU* 5.5 0.2 - - + -
137A ILE* 4.6 18.8 - - + -
140A SER* 6.1 3.1 - - - +
142A GLY 5.2 5.2 - - - +
143A TRP* 3.7 39.2 - - + -
146A PHE* 4.2 20.4 - - + -
149A LEU* 5.8 2.5 - - + -
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Residues in contact with VAL 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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48A ALA* 3.2 33.0 - - - +
52A PHE* 3.9 24.2 - - + -
92A TRP* 3.0 19.3 + - + +
93A GLY* 3.8 7.6 - - - +
95A LEU* 1.3 73.5 - - - +
97A ALA* 1.3 56.0 + - - +
99A PHE* 3.2 6.0 + - - +
100A VAL* 2.8 33.8 + - - +
146A PHE* 3.8 29.6 - - + -
217B ASP* 6.0 3.4 - - - +
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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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52A PHE* 6.3 0.4 - - - -
63A LEU* 5.7 4.7 - - + -
82A SER* 4.4 9.4 - - - -
93A GLY 2.9 19.9 + - - +
94A ARG* 3.7 9.2 - - + +
96A VAL* 1.3 76.6 - - - +
98A PHE* 1.3 58.6 + - - +
100A VAL* 3.3 11.8 - - + +
101A PHE* 2.9 40.6 + - + +
209B LEU* 4.8 16.8 - - + -
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Residues in contact with PHE 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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79A THR* 3.7 23.7 - - + +
80A GLN* 5.8 0.7 - - - -
82A SER* 3.6 22.8 - - - -
83A ASP* 3.6 28.7 - - + -
86A PHE* 3.8 17.9 - + + -
94A ARG 2.9 17.3 + - - +
95A LEU* 3.7 6.5 - - + +
97A ALA* 1.3 76.6 - - - +
99A PHE* 1.3 62.1 + - - +
101A PHE* 3.9 1.2 - - - +
102A GLY* 3.3 16.3 + - - -
124A TRP 6.2 0.2 - - - -
125A MET* 4.0 42.8 - - + +
128A TYR* 4.1 27.4 - + + -
129A LEU* 5.2 9.9 - - + -
133A LEU* 5.3 3.1 - - + -
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Residues in contact with PHE 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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13A VAL* 4.8 17.5 - - + -
16A PHE* 3.9 36.3 - + + -
45A MET* 4.1 33.0 - - + -
48A ALA* 3.7 30.7 - - + -
49A GLY 5.3 0.2 - - - -
95A LEU 3.1 17.5 + - - +
96A VAL* 3.6 4.3 - - - +
98A PHE* 1.3 75.6 - - - +
100A VAL* 1.3 64.1 + - - +
102A GLY* 3.4 1.6 + - - -
103A ALA* 2.8 35.8 + - + +
125A MET* 4.5 16.4 - - + +
143A TRP* 4.7 23.3 - + + -
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Residues in contact with VAL 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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16A PHE* 6.4 0.4 - - - -
48A ALA 4.3 5.8 - - - +
49A GLY* 4.2 9.4 - - - -
52A PHE* 3.7 35.2 - - + -
60A PHE* 3.8 24.7 - - + -
63A LEU* 6.1 3.8 - - + -
96A VAL 2.8 23.4 + - - +
97A ALA* 3.3 15.3 - - + +
99A PHE* 1.3 76.3 - - - +
101A PHE* 1.3 66.6 + - + +
103A ALA* 4.3 5.8 - - + -
104A ALA* 2.8 37.0 + - + +
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Residues in contact with PHE 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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63A LEU* 4.1 31.0 - - + -
64A ALA* 6.0 5.8 - - + -
78A PHE* 3.7 44.4 - + + -
79A THR* 4.4 8.1 - - - -
81A VAL* 4.1 17.9 - - + -
82A SER* 3.6 19.7 - - - +
97A ALA* 2.9 28.5 + - + +
98A PHE 3.9 3.1 - - - +
100A VAL* 1.3 82.3 - - + +
102A GLY* 1.3 62.0 + - - +
104A ALA* 3.9 1.9 - - - +
105A LEU* 3.1 39.2 + - + +
209B LEU* 4.8 7.4 - - + -
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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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79A THR* 4.7 7.9 - - - +
98A PHE 3.3 11.3 + - - -
99A PHE 3.8 1.8 - - - -
101A PHE* 1.3 80.4 - - - +
103A ALA* 1.3 51.8 + - - +
105A LEU* 3.3 3.0 + - - +
106A CYS* 2.7 44.9 + - - -
121A VAL* 4.6 10.8 - - - -
122A GLN* 5.3 0.4 - - - -
125A MET* 4.3 17.5 - - - -
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Residues in contact with ALA 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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13A VAL* 6.2 2.5 - - + -
16A PHE* 4.1 29.2 - - + -
17A VAL* 4.6 11.0 - - + +
99A PHE* 2.8 27.0 + - + +
100A VAL* 3.9 5.8 - - + +
102A GLY* 1.3 75.9 - - - +
104A ALA* 1.3 56.5 + - - +
106A CYS* 3.8 4.5 - - - +
107A ALA* 2.8 33.6 + - - +
122A GLN* 6.1 0.4 - - - +
125A MET* 5.4 0.8 - - - +
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Residues in contact with ALA 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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60A PHE* 5.4 16.6 - - + -
100A VAL* 2.8 27.5 + - + +
101A PHE* 3.9 3.6 - - - +
103A ALA* 1.3 73.3 - - - +
105A LEU* 1.3 68.5 + - + +
107A ALA* 3.4 5.2 + - - +
108A GLU* 3.0 25.0 + - - +
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Residues in contact with LEU 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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75A GLN* 3.2 44.4 - - + +
78A PHE* 4.0 23.1 - - + -
101A PHE* 3.1 34.3 + - + +
102A GLY 3.9 2.9 - - - +
104A ALA* 1.3 80.5 - - + +
106A CYS* 1.3 55.5 + - - +
108A GLU* 3.3 27.8 + - - +
109A SER* 2.7 39.6 + - - +
117A LEU* 5.9 0.4 - - + -
121A VAL* 5.9 0.7 - - + -
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Residues in contact with CYS 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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17A VAL* 4.9 8.7 - - + -
102A GLY 2.7 28.0 + - - +
103A ALA* 3.8 5.4 - - - +
105A LEU* 1.3 73.1 - - - +
107A ALA* 1.3 52.7 + - - +
109A SER* 3.1 2.2 + - - -
110A VAL* 2.8 41.7 + - + +
118A VAL* 3.8 21.0 - - + +
121A VAL* 3.9 22.2 - - - -
122A GLN* 3.0 40.8 - - - +
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Residues in contact with ALA 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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17A VAL* 3.7 31.1 - - + +
20A LYS* 5.1 9.6 - - + -
21A LEU* 4.3 11.7 - - + +
24A LYS* 5.5 0.5 + - - -
103A ALA 2.8 22.0 + - - +
104A ALA* 3.8 5.6 - - - +
106A CYS* 1.3 72.8 - - - +
108A GLU* 1.3 61.7 + - - +
110A VAL* 3.5 2.8 + - - +
111A ASN* 3.3 20.4 + - - +
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Residues in contact with GLU 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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24A LYS* 6.2 0.4 - - - +
104A ALA 3.0 17.1 + - - +
105A LEU* 3.5 24.7 - - - +
107A ALA* 1.3 75.3 - - - +
109A SER* 1.3 65.3 + - - +
111A ASN* 3.1 9.6 + - - +
112A LYS* 2.6 66.3 + - + +
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Residues in contact with SER 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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105A LEU* 2.7 27.5 + - - +
106A CYS* 4.3 0.6 - - - -
108A GLU* 1.3 84.2 + - - +
110A VAL* 1.3 58.3 + - - +
112A LYS* 3.1 11.0 + - - +
113A GLU 3.1 5.0 + - - -
114A MET* 2.7 43.9 + - - +
117A LEU* 3.6 21.4 - - - +
118A VAL* 3.5 22.4 - - - -
121A VAL* 6.1 0.2 - - - +
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Residues in contact with VAL 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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17A VAL* 4.4 15.7 - - + -
21A LEU* 4.5 20.4 - - + -
106A CYS 2.8 24.3 + - - +
107A ALA* 3.7 6.7 - - - +
109A SER* 1.3 75.5 - - - +
111A ASN* 1.3 63.3 + - - +
113A GLU* 3.2 12.8 + - - +
114A MET 4.7 2.5 - - - +
115A GLU* 5.0 12.8 - - - +
118A VAL* 3.9 21.3 - - + -
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Residues in contact with ASN 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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21A LEU* 4.1 16.5 - - + +
24A LYS* 3.8 23.4 + - - +
107A ALA 3.3 9.7 + - - +
108A GLU* 3.1 10.8 + - - +
110A VAL* 1.3 76.6 - - - +
112A LYS* 1.3 62.9 + - - +
113A GLU* 3.1 9.1 + - - +
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Residues in contact with LYS 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 GLU* 2.6 56.3 + - + +
109A SER* 3.1 11.4 + - - +
111A ASN* 1.3 80.8 - - - +
113A GLU* 1.3 70.7 + - - +
114A MET* 3.2 11.8 + - + +
117A LEU* 6.2 1.4 - - - +
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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