Contacts of the helix formed by residues 89 - 109 (chain G) in PDB entry 2H4C
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 89 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B PHE* 5.3 0.7 - - - -
58G ASP* 5.4 1.6 + - - +
59G CYS* 5.4 0.4 - - - -
86G ASP* 3.6 3.0 + - - +
88G ASN* 1.3 82.3 - - - +
90G LEU* 1.3 66.8 + - - +
91G CYS* 3.3 12.7 + - - +
92G LEU* 2.8 58.6 - - + +
93G LYS* 3.3 22.3 + - - +
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Residues in contact with LEU 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B SER* 6.1 0.2 - - - +
122B ILE* 6.6 0.2 - - + -
124B PHE* 3.6 52.9 - - + -
58G ASP* 3.9 24.0 - - + +
88G ASN 3.6 2.9 + - - -
89G ASN* 1.3 77.9 + - - +
91G CYS* 1.3 65.0 + - - +
94G THR* 2.5 33.5 + - + +
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Residues in contact with CYS 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G VAL* 3.6 20.0 - - - +
58G ASP* 3.2 29.4 - - + +
59G CYS* 2.0 60.8 - - + -
89G ASN* 3.3 8.5 + - - +
90G LEU* 1.3 79.6 - - - +
92G LEU* 1.3 68.1 + - - +
94G THR* 3.8 2.0 - - - -
95G VAL* 3.0 26.4 + - - +
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Residues in contact with LEU 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G CYS* 5.3 1.6 - - - -
71G ALA* 3.3 33.0 - - + -
72G THR 3.8 22.9 - - - +
73G TYR* 3.9 12.8 - - + +
86G ASP* 3.7 22.4 - - - +
89G ASN* 2.8 36.4 - - + +
91G CYS* 1.3 71.1 - - + +
93G LYS* 1.3 66.4 + - - +
95G VAL* 2.8 18.6 + - + +
96G CYS* 2.9 10.0 + - - +
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Residues in contact with LYS 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PHE* 4.6 19.3 - - + -
84G CYS* 3.5 22.8 + - + +
86G ASP* 3.5 36.1 + - + +
88G ASN* 5.4 2.0 - - - -
89G ASN 3.3 19.0 + - - +
92G LEU* 1.3 75.9 - - - +
94G THR* 1.3 57.7 + - - +
96G CYS* 2.5 33.9 + - - +
97G GLU* 2.9 27.9 + - + +
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Residues in contact with THR 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PHE* 3.3 26.5 - - + -
51G CYS* 6.0 2.0 - - - -
55G VAL* 4.5 17.3 - - + -
90G LEU* 2.5 28.6 + - + +
91G CYS* 3.8 3.4 - - - -
92G LEU 3.2 0.8 - - - -
93G LYS* 1.3 77.8 - - - +
95G VAL* 1.3 62.2 + - - +
97G GLU* 3.0 24.1 + - + +
98G CYS* 3.3 15.3 + - - -
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Residues in contact with VAL 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ASN 5.2 0.4 - - - +
52G TYR* 4.5 8.7 - - + +
55G VAL* 3.3 26.5 - - + -
59G CYS* 4.6 3.4 - - - -
61G ASN 5.2 0.2 - - - -
68G PRO* 3.7 40.6 - - + +
71G ALA* 5.4 5.6 - - + -
73G TYR* 4.2 16.6 - - + -
91G CYS* 3.0 24.1 + - - +
92G LEU* 2.8 15.2 + - - +
94G THR* 1.3 73.0 - - - +
96G CYS* 1.3 60.9 + - - +
97G GLU 3.1 1.1 + - - -
98G CYS* 3.5 13.6 + - - +
99G ASP* 3.5 18.2 - - - +
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Residues in contact with CYS 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G MET* 4.2 3.4 - - - +
73G TYR* 3.3 48.9 - - + -
74G SER 3.6 6.7 - - - +
75G TYR* 3.8 5.6 - - - -
84G CYS* 2.0 62.3 - - + -
92G LEU 2.9 4.3 + - - +
93G LYS* 2.5 25.1 + - - +
95G VAL* 1.3 71.3 - - - +
97G GLU* 1.3 55.6 + - - -
99G ASP* 4.3 1.3 - - - +
100G ARG* 3.1 18.6 + - - +
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Residues in contact with GLU 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G CYS* 3.7 20.6 - - - +
93G LYS* 2.9 31.3 + - + +
94G THR* 3.0 19.4 + - + +
96G CYS* 1.3 77.9 - - - +
98G CYS* 1.3 67.2 + - - +
99G ASP 3.2 1.3 - - - -
100G ARG* 2.8 37.0 + - - +
101G ALA* 2.8 28.3 + - - +
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Residues in contact with CYS 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G HIS* 3.5 12.5 - - + +
51G CYS* 2.0 62.5 - - + -
52G TYR* 3.6 26.9 - - + -
55G VAL* 4.2 7.6 - - - -
94G THR 3.3 11.4 + - - -
95G VAL* 3.5 3.3 + - - +
97G GLU* 1.3 82.1 - - - +
99G ASP* 1.3 59.1 + - - +
101G ALA* 3.9 3.6 - - - +
102G ALA* 2.9 28.4 + - - +
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Residues in contact with ASP 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ASN 3.7 3.1 - - - +
5G PHE* 2.9 45.8 + - + +
8G MET* 4.1 6.6 - - + +
48G HIS* 3.3 5.5 + - - -
52G TYR* 2.7 27.5 + - - -
73G TYR* 2.7 34.8 + - - +
95G VAL 3.5 12.0 + - - +
96G CYS 4.3 2.7 - - - +
97G GLU 3.2 0.2 - - - -
98G CYS* 1.3 75.5 - - - +
100G ARG* 1.3 61.2 + - - +
103G ALA* 3.0 26.5 + - - +
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Residues in contact with ARG 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G MET* 4.6 2.2 - - - +
81G ASP* 4.3 10.9 + - - -
82G ILE* 3.8 55.2 + - + +
84G CYS* 4.4 5.3 - - - +
96G CYS 3.1 17.2 + - - +
97G GLU* 2.8 34.5 + - - +
99G ASP* 1.3 79.2 - - - +
101G ALA* 1.3 72.6 + - - +
103G ALA* 3.2 7.6 + - - +
104G ILE* 3.4 34.7 + - + +
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Residues in contact with ALA 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G VAL* 6.6 0.4 - - + -
97G GLU* 2.8 18.5 + - - +
98G CYS* 4.0 3.4 - - - +
100G ARG* 1.3 79.8 - - - +
102G ALA* 1.3 61.6 + - - +
104G ILE* 3.3 10.0 + - - +
105G CYS* 3.0 24.6 + - - +
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Residues in contact with ALA 102 (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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5G PHE* 3.6 15.0 - - + -
44G CYS* 3.9 10.3 - - - +
48G HIS* 3.4 32.8 - - + -
98G CYS 2.9 18.6 + - - +
101G ALA* 1.3 77.2 - - - +
103G ALA* 1.3 57.4 + - - +
105G CYS* 3.7 5.1 - - - +
106G LEU* 3.0 38.4 + - + +
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Residues in contact with ALA 103 (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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5G PHE* 4.4 0.6 - - - -
8G MET* 3.5 24.7 - - + -
9G ILE* 3.5 15.9 - - + +
12G MET* 3.2 33.2 - - + +
13G THR* 5.0 0.3 - - - +
82G ILE* 4.5 2.2 - - + -
99G ASP 3.0 18.3 + - - +
100G ARG 3.2 4.5 + - - +
102G ALA* 1.3 75.4 - - - +
104G ILE* 1.3 57.3 + - - +
106G LEU* 3.8 1.5 - - - +
107G GLY 2.9 24.3 + - - -
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Residues in contact with ILE 104 (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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12G MET* 3.5 25.1 - - - -
81G ASP* 6.2 0.2 - - - +
82G ILE* 4.7 4.9 - - + -
100G ARG* 3.5 42.6 - - + +
101G ALA* 3.3 9.4 + - - +
103G ALA* 1.3 72.7 - - - +
105G CYS* 1.3 67.0 + - - +
107G GLY* 3.2 2.3 + - - -
108G GLN* 2.8 52.4 + - + +
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Residues in contact with CYS 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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40G ALA 4.3 2.0 - - - -
43G ARG* 4.9 1.1 - - - -
44G CYS* 2.0 54.1 - - + -
47G VAL* 6.2 1.3 - - - -
101G ALA 3.0 13.8 + - - +
102G ALA* 3.7 4.9 - - - +
104G ILE* 1.3 79.7 - - - +
106G LEU* 1.3 65.0 + - - +
108G GLN* 2.7 18.9 + - - +
109G ASN* 2.9 28.4 + - - +
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Residues in contact with LEU 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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5G PHE* 4.6 6.3 - - + -
9G ILE* 3.7 40.4 - - + -
13G THR* 4.2 2.5 - - - -
22G TYR* 4.1 32.0 + - + +
41G THR* 3.6 20.8 - - + +
44G CYS* 2.9 31.3 - - + -
45G CYS* 4.0 17.3 - - - -
102G ALA* 3.0 24.8 + - + +
103G ALA 3.8 2.7 - - - +
105G CYS* 1.3 72.5 - - - +
107G GLY* 1.3 64.8 + - - +
109G ASN* 2.9 15.3 + - - +
110G VAL* 3.5 15.2 + - - +
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Residues in contact with GLY 107 (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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12G MET* 4.7 2.2 - - - -
13G THR* 3.1 34.4 - - - +
103G ALA 2.9 19.1 + - - -
104G ILE 3.5 4.7 - - - -
106G LEU* 1.3 73.3 - - - +
108G GLN* 1.3 57.3 + - - +
110G VAL* 3.3 19.6 - - - +
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Residues in contact with GLN 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G ILE* 2.8 36.9 + - + +
105G CYS* 2.7 21.2 + - - +
107G GLY* 1.3 75.5 - - - -
109G ASN* 1.3 61.4 + - - +
110G VAL* 3.4 2.8 + - - +
111G ASN* 3.1 14.9 + - - +
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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
----------------------------------------------------------
40G ALA* 3.3 32.3 + - - +
41G THR* 2.9 34.4 + - + +
44G CYS* 3.6 0.8 - - - -
105G CYS* 2.9 39.2 + - - +
106G LEU 2.9 5.7 + - - +
108G GLN* 1.3 82.2 - - - +
110G VAL* 1.3 59.2 + - - +
111G ASN* 3.4 8.0 - - - +
112G THR* 3.3 17.2 - - + +
113G TYR 3.5 2.1 + - - -
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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
------------------------------------------------------------
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