Contacts of the helix formed by residues 92 - 109 (chain G) in PDB entry 1HNW
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 SER 92 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G GLU 4.2 1.2 + - - -
91G VAL* 1.3 75.0 - - - +
93G PRO* 1.3 75.9 - - - +
94G ARG* 3.5 8.5 + - - +
95G ARG* 2.8 24.7 + - - +
96G GLN* 2.9 19.8 + - - +
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Residues in contact with PRO 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G LYS* 5.2 2.3 + - - -
91G VAL 3.6 2.1 - - - +
92G SER* 1.3 86.5 - - - +
94G ARG* 1.3 72.5 + - + +
96G GLN* 3.4 15.6 + - + +
97G GLN* 3.3 17.8 + - - +
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Residues in contact with ARG 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1376A U 3.1 38.0 + - - -
1377A A 3.3 32.8 + - - +
9G VAL* 3.4 45.5 - - + +
12G LEU* 6.2 1.6 - - - +
92G SER* 3.1 8.7 - - - +
93G PRO* 1.3 87.1 - - + +
95G ARG* 1.3 66.6 + - - +
97G GLN* 3.3 28.1 + - - +
98G SER* 3.4 21.3 + - - -
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Residues in contact with ARG 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938A A 3.3 25.4 + - - -
939A G 3.2 30.9 + - - -
1376A U 5.6 0.2 + - - -
1377A A 5.0 12.8 + - - +
74G GLU* 2.9 38.6 + - - -
76G ARG* 4.6 18.3 - - - +
91G VAL* 3.6 12.1 - - + +
92G SER* 2.8 24.1 + - - +
94G ARG* 1.3 72.5 - - - +
96G GLN* 1.3 69.9 + - - +
98G SER* 2.9 22.1 + - - -
99G LEU* 3.0 34.5 + - + +
102G ARG* 5.2 1.4 - - - +
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Residues in contact with GLN 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G LYS* 3.8 30.9 + - + +
71G PRO* 3.1 30.6 + - + +
72G ARG* 4.5 9.5 + - - +
91G VAL* 2.6 38.3 + - + +
92G SER 2.9 14.0 + - - +
93G PRO* 3.5 15.1 - - - +
95G ARG* 1.3 73.7 - - - +
97G GLN* 1.3 63.8 + - - +
99G LEU* 3.0 7.7 + - - +
100G ALA* 3.0 22.3 + - - +
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Residues in contact with GLN 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1376A U 5.2 2.6 + - - -
21G VAL* 6.2 0.2 - - - +
22G LEU* 3.4 27.1 - - + +
25G ALA* 4.3 9.3 - - - +
66G VAL* 5.6 2.0 - - + -
70G LYS* 4.0 20.1 - - - +
93G PRO 3.3 8.7 + - - +
94G ARG* 3.7 26.9 - - - +
95G ARG 3.2 0.8 - - - -
96G GLN* 1.3 78.1 - - - +
98G SER* 1.3 66.6 + - - +
99G LEU 3.2 0.2 + - - -
100G ALA* 3.7 1.9 - - - +
101G LEU* 3.1 46.2 + - + +
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Residues in contact with SER 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1376A U 2.8 34.1 + - - -
1377A A 5.3 1.0 + - - -
29G LYS* 4.8 3.3 - - - -
94G ARG* 3.4 25.7 + - - -
95G ARG* 2.9 19.2 + - - -
97G GLN* 1.3 77.6 - - - +
99G LEU* 1.3 62.0 + - - +
101G LEU* 4.0 3.9 - - - +
102G ARG* 3.1 41.2 + - - +
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Residues in contact with LEU 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939A G 4.2 7.4 - - - +
71G PRO* 3.6 24.9 - - + -
74G GLU* 4.6 7.0 - - - +
91G VAL* 4.2 8.1 - - + -
95G ARG* 3.0 61.4 + - + +
96G GLN 3.4 3.4 - - - +
98G SER* 1.3 73.9 - - - +
100G ALA* 1.3 57.3 + - - +
102G ARG* 3.0 16.1 + - - +
103G TRP* 2.6 68.4 + - + +
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Residues in contact with ALA 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G VAL* 4.0 15.5 - - + +
69G VAL* 3.6 34.6 + - + +
70G LYS* 3.8 17.7 - - + -
96G GLN 3.0 9.3 + - - +
97G GLN 3.7 7.4 - - - +
99G LEU* 1.3 79.2 - - - +
101G LEU* 1.3 54.3 + - + +
103G TRP* 3.0 2.3 + - - +
104G LEU* 2.8 39.6 + - - +
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Residues in contact with LEU 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1376A U 6.0 0.9 - - - +
22G LEU* 4.0 10.5 - - + -
25G ALA* 3.7 23.8 - - + -
26G PHE* 3.7 32.7 - - + +
29G LYS* 4.5 13.5 - - + -
62G PHE* 4.4 1.3 - - + -
66G VAL* 3.8 25.8 - - + -
97G GLN* 3.1 44.5 + - + +
98G SER* 4.0 4.5 - - - +
100G ALA* 1.3 78.6 - - + +
102G ARG* 1.3 65.1 + - - +
104G LEU* 3.0 15.5 + - + +
105G VAL* 3.1 17.7 + - - +
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Residues in contact with ARG 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939A G 2.9 61.2 + - - -
940A C 3.1 26.4 + - - +
1376A U 4.4 10.9 - - - -
29G LYS* 3.8 22.8 - - + +
95G ARG* 5.2 1.0 - - - +
98G SER* 3.1 27.6 + - - +
99G LEU* 3.0 16.9 + - - +
101G LEU* 1.3 78.9 - - - +
103G TRP* 1.3 69.0 + - + +
105G VAL* 3.6 3.3 + - - +
106G GLN* 3.0 52.7 + - + +
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Residues in contact with TRP 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G VAL* 3.2 30.1 - - + -
71G PRO* 3.2 45.5 - - + -
99G LEU* 2.6 46.0 + - + +
100G ALA 3.3 3.4 - - - +
102G ARG* 1.3 78.9 - - + +
104G LEU* 1.3 58.1 + - - +
106G GLN* 3.6 19.2 - - - +
107G ALA* 2.8 35.0 + - - +
134G ALA* 4.5 4.5 - - - -
137G LYS* 3.9 28.2 + - + +
138G LYS* 3.7 17.7 - - + -
141G VAL* 3.9 28.7 - - + -
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Residues in contact with LEU 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G PHE* 3.7 24.2 - - + -
62G PHE* 5.2 0.2 - - + -
65G ALA* 4.5 0.9 - - + -
66G VAL* 4.2 27.4 - - + +
69G VAL* 3.3 32.5 - - + -
100G ALA 2.8 22.8 + - - +
101G LEU* 3.0 6.5 + - - +
103G TRP* 1.3 72.9 - - - +
105G VAL* 1.3 54.7 + - - +
107G ALA* 3.6 0.5 - - - +
108G ALA* 2.7 39.0 + - - +
123G GLU* 4.1 10.3 - - + +
124G LEU* 4.4 16.6 - - + -
127G ALA* 4.2 11.0 - - + -
134G ALA* 3.3 18.8 - - + -
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Residues in contact with VAL 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1240A U 3.9 8.5 - - - +
26G PHE* 3.8 18.1 - - + -
29G LYS* 3.7 39.0 - - + +
30G ILE* 3.7 26.7 - - + -
32G ARG* 5.6 1.3 - - - +
101G LEU 3.1 6.9 + - - +
102G ARG* 4.1 3.1 - - - +
104G LEU* 1.3 78.0 - - - +
106G GLN* 1.3 59.1 + - + +
108G ALA* 3.5 6.6 - - - +
109G ASN* 3.0 43.8 + - - +
120G ILE* 4.9 2.9 - - + -
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Residues in contact with GLN 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940A C 5.1 1.7 + - - -
102G ARG* 3.0 41.0 + - + +
103G TRP* 3.6 21.2 - - - +
105G VAL* 1.3 75.4 - - + +
107G ALA* 1.3 68.0 + - - +
108G ALA 3.0 1.1 - - - -
109G ASN* 3.0 16.9 + - - +
110G GLN* 3.2 17.2 + - + +
137G LYS* 3.4 25.0 - - - +
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Residues in contact with ALA 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G TRP 2.8 20.5 + - - +
104G LEU 3.8 0.9 - - - +
106G GLN* 1.3 74.7 - - - +
108G ALA* 1.3 61.9 + - - +
110G GLN* 3.3 22.3 + - - +
111G ARG* 3.6 6.6 + - - +
123G GLU* 3.3 14.5 - - - +
133G GLY* 3.6 11.6 - - - +
134G ALA* 3.3 31.2 - - - +
137G LYS* 4.7 10.4 - - - +
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Residues in contact with ALA 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G PHE* 6.2 0.7 - - + -
104G LEU 2.7 20.3 + - - +
105G VAL* 3.5 8.3 - - - +
107G ALA* 1.3 75.0 - - - +
109G ASN* 1.3 59.1 + - - +
110G GLN 3.0 7.3 + - - -
111G ARG* 3.2 9.9 + - - +
119G ARG* 2.9 40.0 - - + +
120G ILE* 4.3 11.9 - - + +
123G GLU* 3.8 25.3 - - + +
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Residues in contact with ASN 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1240A U 2.9 35.4 + - - -
32G ARG* 3.8 10.1 - - - +
105G VAL* 3.0 30.8 + - - +
106G GLN* 3.0 8.8 + - - +
108G ALA* 1.3 76.8 - - - +
110G GLN* 1.3 65.7 + - - +
111G ARG 3.3 3.6 - - - +
119G ARG* 3.0 37.8 + - - +
120G ILE* 6.1 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
------------------------------------------------------------
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