Contacts of the helix formed by residues 62 - 76 (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 THR 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B MET* 3.8 13.2 - - + +
44B PRO 4.6 1.6 - - - +
45B GLY* 3.6 34.8 - - - +
46B THR 3.8 0.7 - - - -
47B ASN 3.1 8.5 + - - +
48B ALA* 3.2 39.7 + - + +
61B PHE* 1.3 74.8 - - - +
63B ILE* 1.3 57.8 + - - +
64B ASP* 2.7 24.1 + - - -
65B ARG* 2.9 8.8 + - - +
66B ALA* 2.7 32.4 + - - +
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 3.8 15.6 - - + +
43B MET 4.3 4.9 - - - +
44B PRO* 5.3 0.4 - - + -
45B GLY 4.6 7.7 + - - +
62B THR* 1.3 72.2 - - - +
64B ASP* 1.3 58.1 + - + +
66B ALA* 3.5 8.5 + - - +
67B VAL* 3.2 28.3 + - + +
103B ILE* 3.8 30.7 - - + +
106B GLN* 4.1 20.2 - - + +
107B ALA* 3.8 28.2 - - + +
110B ALA* 3.7 27.4 - - + -
111B ILE* 5.3 0.5 - - - +
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Residues in contact with ASP 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLY 4.4 0.9 - - - +
46B THR* 3.3 21.3 - - - +
47B ASN* 3.1 28.4 + - - +
62B THR* 2.7 21.8 + - - -
63B ILE* 1.3 80.2 - - - +
65B ARG* 1.3 74.3 + - - +
67B VAL* 3.5 9.9 - - - +
68B GLU* 3.3 20.3 + - - +
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Residues in contact with ARG 65 (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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47B ASN* 3.9 31.5 + - - +
49B VAL* 3.3 37.5 - - + +
61B PHE* 3.7 17.0 - - + -
62B THR* 2.9 15.2 + - - +
64B ASP* 1.3 93.4 + - - +
66B ALA* 1.3 60.8 + - - +
67B VAL 3.3 0.7 - - - -
68B GLU* 3.0 45.6 + - - +
69B GLU* 3.0 24.8 + - - +
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Residues in contact with ALA 66 (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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40B LEU* 4.0 21.0 - - + +
42B VAL* 4.3 10.1 - - + -
61B PHE* 4.2 10.2 - - + -
62B THR 2.7 15.7 + - - +
63B ILE* 3.5 12.1 - - - +
65B ARG* 1.3 74.7 - - - +
67B VAL* 1.3 59.2 - - - +
69B GLU* 3.2 7.6 + - - +
70B CYS* 2.9 34.6 + - - -
107B ALA* 5.5 0.4 - - + -
111B ILE* 4.5 11.9 - - + -
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE 3.2 14.9 + - - +
64B ASP* 3.5 11.9 - - - +
66B ALA* 1.3 76.2 - - - +
68B GLU* 1.3 62.0 + - - +
70B CYS* 3.1 6.1 + - - +
71B LYS* 3.1 47.4 + - - +
110B ALA* 4.0 34.5 - - + +
111B ILE* 4.1 12.1 - - + +
114B ALA* 3.6 22.0 - - + -
115B VAL* 4.9 0.5 - - - +
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Residues in contact with GLU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PHE* 4.5 1.2 - - - -
64B ASP 3.3 11.3 + - - +
65B ARG* 3.0 51.3 + - + +
66B ALA 3.3 0.4 - - - -
67B VAL* 1.3 78.9 - - - +
69B GLU* 1.3 75.9 + - - +
71B LYS* 3.5 14.5 + - - +
72B GLU* 3.3 24.3 + - - +
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Residues in contact with GLU 69 (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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38B PHE* 4.5 12.4 - - + -
40B LEU* 4.5 4.9 - - + -
61B PHE* 3.4 37.3 - - + -
65B ARG 3.0 12.9 + - - +
66B ALA* 3.4 11.0 - - - +
68B GLU* 1.3 87.9 - - - +
70B CYS* 1.3 53.1 + - - +
72B GLU* 3.1 7.3 + - - +
73B LEU* 2.7 50.3 + - + +
321B LYS* 2.7 40.8 + - - +
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Residues in contact with CYS 70 (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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40B LEU* 3.7 21.8 - - - -
66B ALA 2.9 25.3 + - - +
67B VAL* 3.1 6.0 + - - +
69B GLU* 1.3 72.9 - - - +
71B LYS* 1.3 60.2 + - - +
73B LEU* 3.7 11.3 - - - +
74B TYR* 2.9 32.4 + - - +
81B ILE* 3.8 13.0 - - - -
111B ILE* 3.8 31.4 - - + -
115B VAL* 4.1 7.3 - - + +
118B LEU* 3.7 15.0 - - + +
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Residues in contact with LYS 71 (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* 3.1 43.5 + - + +
68B GLU* 3.6 12.4 - - - +
70B CYS* 1.3 74.5 - - - +
72B GLU* 1.3 62.1 + - - +
74B TYR* 4.3 1.5 - - - +
75B ASP* 2.9 36.3 + - - +
114B ALA* 4.3 13.3 - - - +
115B VAL* 3.7 19.3 - - + +
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Residues in contact with GLU 72 (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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68B GLU* 3.3 15.1 + - - +
69B GLU* 3.1 11.5 + - - +
71B LYS* 1.3 79.2 - - - +
73B LEU* 1.3 62.9 + - - +
75B ASP* 3.7 5.7 + - - +
76B LEU* 3.3 37.7 + - - +
321B LYS* 3.7 32.7 + - + +
325B LYS* 4.5 10.6 + - - -
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 3.6 47.3 - - + -
40B LEU* 4.4 5.2 - - + -
69B GLU* 2.7 37.1 + - + +
70B CYS* 3.7 11.9 - - - +
71B LYS 3.3 0.2 - - - -
72B GLU* 1.3 72.8 - - - +
74B TYR* 1.3 62.8 + - - +
76B LEU* 3.1 17.2 + - - +
77B GLY 3.3 0.5 + - - -
78B ILE* 3.2 43.9 + - + +
81B ILE* 3.7 20.0 - - + -
118B LEU* 5.1 3.8 - - + -
321B LYS* 3.8 18.8 - - + -
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Residues in contact with TYR 74 (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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70B CYS 2.9 17.0 + - - +
71B LYS* 4.3 1.8 - - - +
73B LEU* 1.3 76.5 - - - +
75B ASP* 1.3 61.3 + - - +
77B GLY* 2.9 20.3 + - - -
78B ILE 3.3 19.5 + - - -
79B GLN* 3.6 23.3 + - - -
115B VAL* 3.8 21.8 - - + -
117B GLU* 3.2 53.6 + - + +
118B LEU* 4.0 15.4 - - + +
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Residues in contact with ASP 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 2.9 30.5 + - - +
72B GLU* 4.0 8.7 - - - +
73B LEU 3.3 0.2 - - - -
74B TYR* 1.3 81.1 - - - +
76B LEU* 1.3 60.6 + - + +
77B GLY 3.2 0.4 + - - -
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Residues in contact with LEU 76 (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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33B VAL* 4.1 16.3 - - - +
72B GLU* 3.3 35.8 + - - +
73B LEU 3.1 9.6 + - - +
75B ASP* 1.3 77.8 - - - +
77B GLY* 1.3 59.3 + - - +
78B ILE 3.7 0.4 - - - -
321B LYS* 3.6 31.9 - - + +
324B ALA* 4.1 18.2 - - + +
325B LYS* 3.7 38.1 - - + +
328B ARG* 4.3 23.0 - - + +
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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