Contacts of the helix formed by residues 102 - 115 (chain B) in PDB entry 2C1H
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 GLY 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B GLU* 3.8 22.7 - - - -
99B ASN* 3.2 14.6 + - - -
100B ASP 3.4 0.6 - - - -
101B ASN* 1.3 82.2 - - - +
103B ILE* 1.3 62.7 + - - -
104B LEU 3.2 2.9 - - - -
105B GLN* 3.0 15.2 + - - +
106B GLN* 2.9 25.1 + - - +
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Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B VAL* 3.7 40.4 - - + +
43B MET 4.3 3.6 - - - -
44B PRO* 3.9 22.0 - - + -
45B GLY 5.4 0.2 - - - +
63B ILE* 3.8 13.3 - - + +
85B GLY* 4.9 0.9 - - - -
86B ILE 4.6 11.7 - - - +
87B PRO* 5.7 1.6 - - + -
88B GLU* 3.3 37.9 + - - +
96B GLU* 4.9 1.0 + - - +
101B ASN 5.0 1.1 - - - +
102B GLY* 1.3 71.9 - - - -
104B LEU* 1.3 58.5 + - - +
106B GLN* 3.6 16.3 - - - +
107B ALA* 2.9 29.1 + - - +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B VAL* 5.4 1.3 - - + -
83B LEU* 4.0 22.9 - - + +
84B PHE 3.5 7.9 - - - +
85B GLY* 3.3 35.8 - - - +
102B GLY 3.2 0.2 - - - -
103B ILE* 1.3 79.6 - - - +
105B GLN* 1.3 66.5 + - - +
107B ALA* 3.3 6.8 + - + +
108B ILE* 3.0 44.1 + - + +
122B THR* 4.0 14.4 - - + -
123B ASP 5.2 2.9 - - - +
129B PHE* 5.1 13.2 - - + -
155B MET* 5.8 0.4 - - + -
159B HIS* 3.4 36.1 - - + +
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Residues in contact with GLN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B GLU 4.8 1.6 - - - +
97B ALA 3.1 22.6 + - - +
99B ASN 2.9 21.7 + - - +
100B ASP* 3.5 20.9 - - - +
102B GLY* 3.0 17.2 + - - +
104B LEU* 1.3 80.2 - - - +
106B GLN* 1.3 61.6 + - - +
108B ILE* 3.5 10.1 + - + -
109B ARG* 3.1 32.6 + - - +
158B SER* 2.7 44.1 + - - +
159B HIS* 4.0 11.6 - - - -
162B ALA* 3.5 9.4 - - + +
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Residues in contact with GLN 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE* 4.1 19.1 - - + +
101B ASN* 3.0 26.5 - - - +
102B GLY 2.9 14.4 + - - +
103B ILE* 3.6 19.5 - - - +
105B GLN* 1.3 74.8 - - - +
107B ALA* 1.3 58.0 + - - +
109B ARG* 3.4 21.1 + - - +
110B ALA* 2.9 31.0 + - - +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B VAL* 4.1 24.5 - - + -
63B ILE* 3.8 23.1 - - + +
83B LEU* 4.7 4.9 - - + -
103B ILE 2.9 17.2 + - - +
104B LEU* 3.5 7.2 - - + +
106B GLN* 1.3 73.8 - - - +
108B ILE* 1.3 58.8 + - - +
110B ALA* 3.9 0.2 - - - +
111B ILE* 2.9 48.0 + - + +
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B LEU* 4.2 9.4 - - + +
104B LEU* 3.0 41.1 + - + +
105B GLN* 3.6 13.7 - - - +
107B ALA* 1.3 73.8 - - - +
109B ARG* 1.3 59.9 + - - +
112B LYS* 2.9 34.4 + - + +
120B ILE* 3.6 13.5 - - + +
122B THR* 3.7 24.0 - - + -
159B HIS* 3.8 17.0 - - + -
162B ALA* 3.7 16.8 - - + -
163B GLY 3.6 7.4 - - - +
164B ALA* 3.4 30.5 - - - +
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Residues in contact with ARG 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ASP* 2.9 33.3 + - - +
101B ASN* 3.7 17.4 - - - +
105B GLN* 3.1 23.3 + - - +
106B GLN* 3.8 23.6 - - - +
108B ILE* 1.3 80.1 - - - +
110B ALA* 1.3 61.7 + - - +
112B LYS* 4.3 2.8 - - - +
113B LYS* 3.4 23.2 + - - +
161B GLU 5.0 2.6 + - - -
162B ALA* 3.4 33.9 - - - +
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE* 3.7 23.8 - - + -
67B VAL* 4.0 14.4 - - + +
106B GLN 2.9 17.7 + - - +
107B ALA 3.9 1.3 - - - +
109B ARG* 1.3 76.3 - - - +
111B ILE* 1.3 64.3 + - - +
113B LYS* 3.3 7.6 + - - +
114B ALA* 3.2 22.9 + - - +
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE 5.3 0.4 - - - +
66B ALA* 4.5 10.1 - - + -
67B VAL* 4.2 20.9 - - + +
70B CYS* 3.8 38.8 - - + -
81B ILE* 4.0 3.4 - - + -
83B LEU* 3.8 35.2 - - + -
107B ALA* 2.9 28.0 + - + +
110B ALA* 1.3 74.6 - - - +
112B LYS* 1.3 58.5 + - - +
114B ALA* 3.2 2.4 + - - +
115B VAL* 2.8 37.0 + - + +
118B LEU* 5.0 3.8 - - + -
120B ILE* 3.8 21.3 - - + -
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Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ILE* 2.9 20.2 + - + +
109B ARG* 4.3 5.2 - - - +
111B ILE* 1.3 76.8 - - - +
113B LYS* 1.3 62.6 + - - +
115B VAL 4.5 3.1 + - - -
116B PRO* 3.3 39.8 + - + +
118B LEU 3.1 18.2 + - - -
120B ILE* 3.7 12.1 - - + +
162B ALA 5.2 0.4 - - - +
163B GLY* 3.5 27.6 - - - +
165B ASP* 2.8 35.8 + - - -
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ARG 3.4 13.5 + - - +
110B ALA* 3.3 10.5 + - - +
111B ILE 3.2 0.8 - - - -
112B LYS* 1.3 80.8 - - - +
114B ALA* 1.3 63.5 + - - +
116B PRO* 3.7 10.4 - - - +
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B VAL* 3.6 30.7 - - + -
71B LYS* 4.3 10.9 - - - +
110B ALA 3.2 11.1 + - - +
111B ILE* 4.0 2.0 - - - +
113B LYS* 1.3 81.4 - - - +
115B VAL* 1.3 67.8 + - + +
116B PRO* 3.3 8.3 - - - +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B VAL* 4.9 0.9 - - + +
70B CYS* 4.1 7.2 - - + -
71B LYS* 3.7 41.1 - - + +
74B TYR* 3.8 40.2 - - + -
111B ILE* 2.8 24.7 + - + +
112B LYS* 4.3 1.7 + - - +
114B ALA* 1.3 79.8 - - + +
116B PRO* 1.3 62.9 - - - +
117B GLU* 3.4 6.2 + - - +
118B LEU* 3.5 28.1 + - + +
120B ILE* 5.7 0.3 - - - +
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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