Contacts of the helix formed by residues 64 - 79 (chain B) in PDB entry 3RMD
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 64 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B ASP* 3.4 30.2 + - + +
32B GLU* 4.4 7.4 - - - +
33B TYR 4.1 8.5 - - - -
35B PRO* 3.9 6.3 - - - -
62B PHE* 3.3 6.3 - - - +
63B ALA* 1.3 83.3 - - - +
65B MET* 1.3 61.9 + - - +
66B ARG* 2.8 13.8 + - - +
67B ASP* 2.6 61.1 + - - +
68B ALA 3.3 8.7 + - - -
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Residues in contact with MET 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLN* 3.2 34.8 - - - +
12B GLY 3.7 7.0 - - - +
13B ASP* 3.5 33.7 + - - +
14B SER 3.7 7.9 - - - +
15B ILE* 3.8 29.2 - - + -
33B TYR* 3.8 19.0 + - + +
35B PRO* 3.8 19.5 - - + +
64B ASN* 1.3 71.0 - - - +
66B ARG* 1.3 64.4 + - - +
68B ALA* 3.3 2.1 + - - +
69B SER* 2.9 24.8 + - - -
88B PHE* 3.5 28.9 - - + -
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Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ASP* 3.1 23.3 + - - +
64B ASN* 2.8 12.2 + - - +
65B MET* 1.3 75.2 - - - +
67B ASP* 1.3 60.6 + - - +
69B SER* 3.1 8.8 + - - +
70B GLN* 2.9 73.6 + - - +
73B LYS* 5.0 2.2 - - - +
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Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 4.0 16.1 - - + -
63B ALA* 3.6 16.3 + - - +
64B ASN* 2.6 41.9 + - - +
66B ARG* 1.3 76.3 - - - +
68B ALA* 1.3 60.7 + - - +
70B GLN* 3.3 6.0 + - - +
71B TRP* 2.8 31.7 + - - +
74B ARG* 4.8 1.9 + - - -
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Residues in contact with ALA 68 (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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35B PRO* 3.7 15.7 - - + -
37B LEU* 4.0 3.7 - - + +
62B PHE* 3.6 33.1 - - + -
64B ASN 3.3 2.6 + - - -
65B MET 3.5 8.1 - - - +
67B ASP* 1.3 79.6 - - - +
69B SER* 1.3 63.3 + - - +
71B TRP* 3.1 5.4 + - - +
72B ILE* 2.9 25.8 + - - +
88B PHE* 3.5 20.9 - - + -
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Residues in contact with SER 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B MET 2.9 19.1 + - - -
66B ARG* 3.1 14.0 + - - +
68B ALA* 1.3 74.6 - - - +
70B GLN* 1.3 63.8 + - - +
72B ILE* 3.0 16.1 + - - +
73B LYS* 3.0 22.8 + - - +
88B PHE* 4.2 12.5 - - - -
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Residues in contact with GLN 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ARG* 2.9 66.1 + - - +
67B ASP* 3.7 6.1 - - - +
69B SER* 1.3 76.6 + - - +
71B TRP* 1.3 62.5 + - - +
73B LYS* 2.6 45.7 + - - +
74B ARG* 3.1 40.5 + - - +
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Residues in contact with TRP 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.5 36.1 - - + -
38B PHE* 3.8 20.6 - - - -
39B ALA* 4.3 6.5 - - + -
60B LYS* 3.5 31.8 - - + +
62B PHE* 3.3 25.8 - + + -
67B ASP 2.8 14.3 + - - +
68B ALA 3.1 9.2 - - - +
69B SER 3.1 0.2 - - - -
70B GLN* 1.3 74.3 - - - +
72B ILE* 1.3 66.8 + - + +
74B ARG* 3.3 27.4 + - + +
75B MET* 2.9 68.9 + - + +
82B ALA* 3.8 17.9 - - + -
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.5 27.1 - - + -
68B ALA 2.9 19.9 + - - +
69B SER* 3.0 14.1 + - - +
71B TRP* 1.3 81.0 - - + +
73B LYS* 1.3 66.6 + - - +
75B MET* 3.4 3.4 + - - +
76B GLU* 3.0 47.0 + - - +
82B ALA* 4.1 15.3 - - + +
86B ASP* 3.9 28.7 - - + -
88B PHE* 4.9 3.8 - - + -
382B GLN* 5.8 0.2 - - + -
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Residues in contact with LYS 73 (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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66B ARG* 5.0 2.2 - - - +
69B SER 3.0 11.5 + - - +
70B GLN* 2.6 46.1 + - - +
72B ILE* 1.3 77.2 - - - +
74B ARG* 1.3 59.3 + - + +
76B GLU* 3.4 5.8 + - - +
77B ASP* 3.0 27.8 + - - +
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Residues in contact with ARG 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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62B PHE* 5.8 0.4 - - - -
67B ASP 4.8 1.6 + - - -
70B GLN* 3.1 33.3 + - - +
71B TRP* 3.4 37.5 - - + +
72B ILE 3.2 0.2 - - - -
73B LYS* 1.3 75.4 - - + +
75B MET* 1.3 67.1 + - + +
77B ASP* 3.0 9.1 + - - +
78B ILE* 3.0 23.6 + - - +
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Residues in contact with MET 75 (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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39B ALA* 3.9 13.7 - - + -
71B TRP* 2.9 66.5 + - + +
72B ILE 3.8 3.6 - - - +
74B ARG* 1.3 74.4 - - + +
76B GLU* 1.3 58.9 + - - +
78B ILE* 3.0 7.6 - - - +
79B GLY 2.9 22.2 + - - -
80B LEU* 3.0 48.8 + - + +
81B GLU 3.3 25.8 - - - +
82B ALA* 4.1 9.4 - - + -
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Residues in contact with GLU 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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72B ILE* 3.0 35.6 + - + +
73B LYS* 3.8 5.3 - - - +
75B MET* 1.3 74.6 - - + +
77B ASP* 1.3 67.2 + - - +
79B GLY* 3.3 11.2 + - - +
80B LEU 4.2 4.3 - - - +
382B GLN* 3.1 45.6 + - - +
383B GLY 4.8 3.7 - - - +
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Residues in contact with ASP 77 (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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73B LYS 3.0 13.4 + - - +
74B ARG* 3.0 13.1 + - - +
76B GLU* 1.3 80.1 - - - +
78B ILE* 1.3 61.8 + - - +
79B GLY* 3.3 0.7 + - - -
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Residues in contact with ILE 78 (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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74B ARG 3.0 10.2 + - - +
75B MET* 3.0 24.2 - - - +
77B ASP* 1.3 78.1 - - - +
79B GLY* 1.3 58.0 + - - +
80B LEU* 3.6 32.5 - - + +
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Residues in contact with GLY 79 (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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75B MET 2.9 4.1 + - - -
76B GLU* 3.3 9.6 + - - -
77B ASP 3.1 4.8 - - - -
78B ILE* 1.3 80.5 - - - +
80B LEU* 1.3 64.3 + - - +
81B GLU 4.2 0.3 + - - -
384B ARG* 5.6 2.4 + - - -
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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