Contacts of the helix formed by residues 98 - 112 (chain A) in PDB entry 2C4P
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 THR 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A GLU* 3.3 26.0 - - - +
12A ASP* 5.9 3.1 - - - +
60A TYR* 4.4 2.2 - - - -
93A TRP* 5.3 0.2 - - - -
96A ALA 3.8 9.4 - - - +
97A LEU* 1.3 76.9 - - - +
99A VAL* 1.3 67.2 + - - +
100A SER* 3.2 14.9 - - - -
101A LYS* 2.9 43.1 + - + +
102A VAL* 3.1 16.7 + - - +
112B ASP* 4.8 8.7 - - - +
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Residues in contact with VAL 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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9A GLU* 2.9 19.0 + - + +
13A LEU* 4.8 7.2 - - + -
23A ALA* 4.9 16.2 - - + -
33A TRP* 5.0 5.8 - - + -
54A VAL* 4.6 26.5 - - + -
56A PHE* 3.6 33.0 - - + -
60A TYR* 3.9 9.3 + - + +
65A PRO* 5.0 7.6 - - + -
67A ILE* 5.8 1.1 - - + -
98A THR* 1.3 71.4 - - - +
100A SER* 1.3 64.1 + - - +
102A VAL* 3.1 22.0 + - + +
103A LEU* 3.1 18.4 + - + +
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Residues in contact with SER 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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9A GLU 4.8 0.3 + - - -
12A ASP* 5.4 2.1 + - - -
13A LEU* 2.7 41.4 + - - +
98A THR* 3.0 12.4 + - - -
99A VAL* 1.3 79.4 - - - +
101A LYS* 1.3 64.9 + - - +
103A LEU* 2.8 28.1 + - - +
104A LEU* 2.9 19.7 - - - +
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Residues in contact with LYS 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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88A ILE* 5.8 0.9 - - + -
96A ALA 6.1 0.4 - - - -
97A LEU* 4.0 28.4 - - + +
98A THR* 2.9 35.9 + - + +
100A SER* 1.3 80.1 - - - +
102A VAL* 1.3 59.6 + - + +
103A LEU 2.9 0.9 + - - -
104A LEU* 3.0 19.2 + - + +
105A SER* 2.7 31.6 + - - +
42B ASP 5.9 2.7 - - - -
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Residues in contact with VAL 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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65A PRO* 4.7 11.0 - - + -
67A ILE* 5.1 11.2 - - + -
88A ILE* 4.2 13.2 - - + -
89A LEU* 3.8 26.2 - - + -
93A TRP* 4.5 17.5 - - + -
97A LEU* 5.6 1.3 - - + -
98A THR 3.1 15.7 + - - +
99A VAL* 3.3 15.0 - - + +
101A LYS* 1.3 76.8 - - + +
103A LEU* 1.3 63.0 + - + +
105A SER* 3.3 8.1 - - - -
106A ILE* 3.0 37.1 + - + +
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Residues in contact with LEU 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 LEU* 5.4 5.6 - - + -
18A PRO* 5.1 7.6 - - + -
21A CYS* 3.7 32.5 - - + -
22A SER* 4.6 4.0 - - - +
23A ALA* 4.6 16.8 - - + +
35A ALA* 4.2 22.7 - - + -
36A THR 5.9 0.9 - - - +
37A ILE* 4.8 9.0 - - + +
52A LEU* 5.8 5.4 - - + -
54A VAL* 6.1 1.8 - - + -
99A VAL* 3.1 22.6 + - + +
100A SER* 2.8 19.6 + - - +
102A VAL* 1.3 78.4 - - + +
104A LEU* 1.3 63.6 + - + +
106A ILE* 3.1 8.0 + - + +
107A CYS* 2.8 28.7 + - - +
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Residues in contact with LEU 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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18A PRO* 5.0 13.0 - - + -
21A CYS* 4.9 10.1 - - - -
100A SER* 2.9 30.1 - - - +
101A LYS* 3.0 25.4 + - + +
103A LEU* 1.3 86.9 - - + +
105A SER* 1.3 57.3 + - - +
107A CYS* 3.3 9.8 - - + +
108A SER* 2.9 36.1 + - - +
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Residues in contact with SER 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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86A LEU* 3.6 10.2 - - - +
88A ILE* 3.1 33.2 - - - +
101A LYS* 2.7 21.4 + - - +
102A VAL 3.3 8.7 - - - -
104A LEU* 1.3 78.8 - - - +
106A ILE* 1.3 56.6 + - - +
108A SER* 3.4 4.5 + - - -
109A LEU* 2.9 27.5 + - - +
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Residues in contact with ILE 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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37A ILE* 5.9 4.0 - - + -
52A LEU* 5.8 2.0 - - + -
67A ILE* 5.9 1.8 - - + -
69A PHE* 4.0 28.3 - - + -
78A ILE* 5.2 1.6 - - + -
84A ILE* 3.8 32.3 - - + -
86A LEU* 3.3 28.0 - - + -
89A LEU* 4.8 2.2 - - + -
102A VAL* 3.0 25.4 + - + +
103A LEU* 3.7 4.9 - - - +
105A SER* 1.3 72.8 - - - +
107A CYS* 1.3 61.3 + - - +
109A LEU* 3.1 11.6 + - + +
110A LEU* 2.8 45.1 + - + +
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Residues in contact with CYS 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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20A HIS* 5.9 4.9 - - - -
21A CYS* 4.5 8.3 - - - -
37A ILE* 3.4 28.9 - - + +
38A MET 4.4 1.1 - - - -
40A PRO* 3.6 30.8 - - - +
103A LEU 2.8 14.0 + - - +
104A LEU* 3.3 17.3 - - - +
106A ILE* 1.3 79.7 - - - +
108A SER* 1.3 60.5 + - - +
110A LEU* 3.5 21.4 - - - +
111A CYS* 3.5 4.3 + - - +
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Residues in contact with SER 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 LEU* 2.9 16.9 + - - +
105A SER* 3.9 4.5 - - - -
107A CYS* 1.3 73.8 - - - +
109A LEU* 1.3 57.2 + - - +
110A LEU 3.1 0.2 - - - -
111A CYS* 3.0 9.3 + - - +
112A ASP* 2.6 38.9 + - - +
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Residues in contact with LEU 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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75A HIS* 2.9 53.0 - - + +
77A ASN* 3.0 22.0 - - + +
78A ILE* 5.5 1.8 - - + -
84A ILE* 4.7 7.0 - - + -
85A CYS 4.7 4.7 - - - +
86A LEU* 3.5 37.0 - - + -
105A SER 2.9 16.2 + - - +
106A ILE* 3.2 27.6 - - + +
108A SER* 1.3 78.3 - - - +
110A LEU* 1.3 59.9 + - + +
112A ASP 3.7 7.6 - - - +
113A PRO* 3.1 14.7 - - + -
114A ASN* 4.6 2.2 - - + +
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Residues in contact with LEU 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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37A ILE* 4.3 28.9 - - + -
39A GLY* 5.3 0.2 - - - -
40A PRO* 4.5 11.0 - - + -
45A TYR* 3.2 32.5 - - + -
50A PHE* 4.9 7.9 - - + -
69A PHE* 4.4 2.7 - - + -
73A ILE* 3.4 32.3 - - + -
75A HIS* 3.4 12.9 - - + +
78A ILE* 4.2 13.0 - - + -
106A ILE* 2.8 39.0 + - + +
107A CYS* 3.5 16.2 - - - +
108A SER 3.1 0.2 - - - -
109A LEU* 1.3 78.6 - - - +
111A CYS* 1.3 63.5 + - - +
113A PRO* 3.9 2.1 - - - +
134A TYR* 4.7 1.6 + - - -
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Residues in contact with CYS 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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40A PRO* 4.1 16.8 - - - -
42A ASP* 5.0 5.6 - - - -
43A SER* 3.6 32.7 - - - -
107A CYS 3.5 3.9 + - - +
108A SER* 3.0 13.6 + - - +
110A LEU* 1.3 80.0 - - - +
112A ASP* 1.3 59.8 + - + +
113A PRO* 3.1 10.0 - - - +
127A TYR* 5.0 1.7 + - - -
134A TYR* 5.9 0.5 - - - -
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Residues in contact with ASP 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 SER* 2.6 17.6 + - - +
109A LEU* 3.2 14.2 - - - +
111A CYS* 1.3 75.3 - - + +
113A PRO* 1.3 65.4 - - - +
127A TYR* 3.7 13.7 + - - -
131A LYS* 5.6 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