Contacts of the helix formed by residues 97 - 112 (chain A) in PDB entry 2C4Y
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A PHE 4.0 8.1 - - - +
96A ALA* 1.3 76.9 - - - +
98A ASN* 1.3 64.9 + - - +
99A SER* 3.0 22.8 + - - -
100A ASP* 3.0 18.5 + - - +
101A CYS* 3.0 21.1 + - - -
66B LYS* 4.2 1.8 - - - +
68B ALA* 3.9 15.2 - - + +
125B ASN* 3.8 4.0 - - - +
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Residues in contact with ASN 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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97A THR* 1.3 74.5 - - - +
99A SER* 1.3 57.5 + - - +
101A CYS* 3.2 4.4 + - - +
102A GLU* 2.9 37.3 + - - +
123B ALA 3.6 13.5 - - - +
124B ALA* 3.7 18.7 + - - +
125B ASN* 3.0 24.0 + - - +
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Residues in contact with SER 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A THR* 3.0 15.6 + - - -
98A ASN* 1.3 77.0 - - - +
100A ASP* 1.3 67.6 + - - +
102A GLU* 3.4 16.7 + - - +
103A LEU* 3.2 23.2 + - - +
68B ALA* 4.8 4.5 - - - +
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Residues in contact with ASP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA* 3.5 10.9 - - + -
97A THR* 3.0 28.7 + - - +
99A SER* 1.3 82.2 + - - +
101A CYS* 1.3 62.7 + - - +
103A LEU* 3.2 21.9 + - - +
104A ILE* 3.4 13.7 + - + +
64B VAL* 5.2 0.7 - - - +
65B PRO 5.5 1.3 - - - +
66B LYS* 2.9 46.2 + - + +
67B VAL* 3.1 13.2 + - - +
68B ALA* 3.1 22.6 + - - +
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Residues in contact with CYS 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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56A ARG* 6.0 0.2 - - - -
92A ILE* 4.2 17.9 - - - -
96A ALA* 4.2 14.6 - - - -
97A THR 3.0 16.6 + - - +
98A ASN* 3.2 8.3 + - - +
100A ASP* 1.3 74.8 - - - +
102A GLU* 1.3 64.8 + - - +
103A LEU 3.1 1.8 - - - -
104A ILE* 3.1 12.2 + - - +
105A VAL* 3.1 24.8 + - - +
122B ILE* 3.4 28.3 - - + +
123B ALA* 3.9 7.2 - - - +
125B ASN* 3.9 23.8 - - - -
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Residues in contact with GLU 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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98A ASN* 2.9 27.0 + - - +
99A SER* 3.6 15.5 - - - +
100A ASP 3.3 0.4 - - - -
101A CYS* 1.3 77.3 - - - +
103A LEU* 1.3 57.2 + - - +
105A VAL* 3.3 5.4 + - + +
106A LYS* 3.0 40.0 + - + +
123B ALA* 3.9 26.9 - - + +
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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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99A SER 3.2 10.4 + - - +
100A ASP* 3.2 15.3 - - - +
102A GLU* 1.3 79.6 - - - +
104A ILE* 1.3 63.6 + - - +
106A LYS* 3.5 8.7 + - + +
107A ALA* 3.1 23.4 + - - +
10B VAL* 4.0 24.2 - - + +
12B ASN* 5.4 4.9 - - - +
18B VAL* 5.9 0.7 - - + -
42B TYR* 3.4 29.6 - - + +
64B VAL* 4.6 5.6 - - + +
65B PRO 4.4 7.2 - - - +
67B VAL* 3.4 32.3 - - + -
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Residues in contact with ILE 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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90A LEU* 3.9 31.6 - - + -
92A ILE* 3.9 26.0 - - + -
96A ALA* 5.6 1.1 - - + -
100A ASP 3.5 15.3 - - - +
101A CYS* 3.1 12.9 + - - +
103A LEU* 1.3 74.3 - - - +
105A VAL* 1.3 65.5 + - + +
107A ALA* 3.2 5.4 + - - +
108A MET* 3.1 31.2 + - + +
64B VAL* 3.9 30.1 - - + -
84B SER* 3.3 28.0 - - - +
86B LEU* 6.0 1.1 - - + -
122B ILE* 5.0 1.8 - - + -
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Residues in contact with VAL 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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101A CYS 3.1 13.6 + - - +
102A GLU* 3.6 8.7 - - - +
103A LEU 3.3 0.2 - - - -
104A ILE* 1.3 77.6 - - - +
106A LYS* 1.3 61.4 + - + +
108A MET* 3.2 15.9 + - + +
109A GLN* 3.0 39.9 + - + +
112B LEU* 4.9 1.1 - - + +
114B ASP* 4.9 4.5 - - - +
119B PRO* 3.7 44.6 - - + +
122B ILE* 3.8 19.3 - - + -
123B ALA* 4.1 8.7 - - + -
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Residues in contact with LYS 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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102A GLU* 3.0 29.3 + - + +
103A LEU* 3.8 10.1 - - + +
105A VAL* 1.3 76.7 - - + +
107A ALA* 1.3 57.1 + - - +
109A GLN* 3.3 17.4 + - - +
110A GLY* 2.9 24.6 + - - -
9B LEU 3.2 7.1 - - - +
10B VAL* 4.0 20.5 - - + -
11B ASP 3.5 20.4 + - - +
12B ASN* 4.0 20.1 + - - +
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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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103A LEU 3.1 14.3 + - - +
104A ILE 3.4 9.2 - - - +
106A LYS* 1.3 75.3 - - - +
108A MET* 1.3 58.7 + - + +
110A GLY 3.4 0.3 + - - -
111A LEU* 2.9 29.7 + - - +
9B LEU* 3.4 34.5 - - + +
10B VAL* 4.1 8.0 - - + +
42B TYR* 5.0 1.1 - - + -
62B VAL* 4.9 5.6 - - + -
64B VAL* 4.1 21.3 - - + -
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Residues in contact with MET 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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60A ILE* 6.4 0.7 - - + -
88A MET* 5.0 6.7 - - - +
90A LEU* 4.2 7.4 - - + -
104A ILE* 3.1 30.1 + - + +
105A VAL* 3.2 18.8 + - + +
107A ALA* 1.3 78.1 - - + +
109A GLN* 1.3 61.5 + - - +
111A LEU* 3.5 11.2 - - + +
112A LEU* 3.5 28.4 + - - +
62B VAL* 6.1 1.3 - - + -
86B LEU* 3.5 40.4 - - + -
112B LEU* 3.9 33.2 - - + -
119B PRO* 6.0 0.4 - - + -
122B ILE* 4.1 25.8 - - + -
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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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105A VAL* 3.0 24.4 + - + +
106A LYS* 3.7 23.3 + - - +
107A ALA 3.2 0.2 - - - -
108A MET* 1.3 75.3 - - - +
110A GLY* 1.3 65.5 + - - +
112A LEU* 3.4 4.2 + - - +
113A LYS* 3.2 22.6 + - - +
112B LEU* 2.8 38.5 + - + +
113B LYS* 3.9 1.2 - - - +
114B ASP* 3.3 36.4 + - - +
119B PRO* 4.9 0.2 - - - +
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Residues in contact with GLY 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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106A LYS 2.9 11.3 + - - -
107A ALA 3.8 0.2 - - - -
109A GLN* 1.3 74.6 - - - +
111A LEU* 1.3 62.4 + - - +
112A LEU 3.4 0.3 + - - -
113A LYS* 3.4 9.6 + - - -
116A ASN* 2.7 30.4 + - - +
7B PHE* 4.3 1.0 - - - -
8B VAL 3.9 8.8 - - - +
9B LEU* 3.3 21.5 - - - -
11B ASP* 5.9 2.9 - - - -
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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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107A ALA 2.9 18.4 + - - +
108A MET* 3.5 7.9 - - - +
110A GLY* 1.3 79.4 - - - +
112A LEU* 1.3 68.1 + - + +
113A LYS 3.8 0.2 + - - -
116A ASN* 4.3 4.5 - - - +
118A ILE* 3.6 29.9 - - + +
119A PRO* 3.3 20.1 - - - +
7B PHE* 4.4 9.4 - - + -
9B LEU* 4.2 12.7 - - + +
44B VAL* 3.7 20.0 - - + -
60B ILE* 4.1 14.8 - - + -
62B VAL* 4.1 22.0 - - + -
86B LEU* 4.8 5.2 - - + -
88B MET* 4.3 17.5 - - - -
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Residues in contact with LEU 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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88A MET* 5.8 1.1 - - + -
108A MET 3.5 7.3 + - - +
109A GLN* 3.4 5.8 + - - +
110A GLY 3.3 0.2 - - - -
111A LEU* 1.3 93.1 - - + +
113A LYS* 1.3 61.8 + - - +
118A ILE* 5.0 12.3 - - + -
119A PRO* 3.7 16.5 - - + +
122A ILE* 5.4 0.4 - - + -
88B MET* 4.7 12.8 - - + -
105B VAL* 5.7 1.6 - - + -
108B MET* 3.9 48.2 - - + +
109B GLN* 2.8 36.4 + - + +
112B LEU* 3.4 33.0 - - + -
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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