Contacts of the helix formed by residues 64 - 79 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C ASP* 3.4 35.9 + - + +
32C GLU* 5.9 2.9 - - + +
33C TYR 4.0 9.6 - - - -
35C PRO* 3.9 6.3 - - - -
62C PHE* 3.3 4.6 - - - +
63C ALA* 1.3 93.6 + - - +
65C MET* 1.3 66.4 + - - +
66C ARG* 3.2 1.1 - - - +
67C ASP* 2.7 49.0 + - - +
68C ALA 3.3 8.0 + - - -
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Residues in contact with MET 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLN* 3.4 30.5 - - - +
12C GLY 4.3 1.6 - - - +
13C ASP* 3.8 28.9 - - - +
15C ILE* 3.7 19.7 - - + -
33C TYR* 3.1 45.8 - - + +
35C PRO* 3.8 17.0 - - + +
64C ASN* 1.3 72.4 - - - +
66C ARG* 1.3 62.7 + - - +
68C ALA* 3.1 2.3 + - - +
69C SER* 2.9 27.9 + - - +
88C PHE* 3.3 33.7 - - + -
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Residues in contact with ARG 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C GLY* 5.3 7.6 + - - +
13C ASP* 2.7 40.8 + - - +
64C ASN* 3.2 3.3 - - - +
65C MET* 1.3 72.8 - - - +
67C ASP* 1.3 61.7 + - - +
69C SER* 3.2 6.3 + - - -
70C GLN* 2.9 37.5 + - + +
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Residues in contact with ASP 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PHE* 3.5 15.0 - - + -
63C ALA* 3.4 16.6 + - - +
64C ASN* 2.7 35.0 + - - +
66C ARG* 1.3 77.6 + - - +
68C ALA* 1.3 56.2 + - - +
70C GLN* 3.3 7.4 + - - +
71C TRP* 2.8 36.4 + - - +
74C ARG* 4.9 1.4 + - - -
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C PRO* 3.5 22.2 - - + -
37C LEU* 3.8 9.1 - - + +
62C PHE* 3.3 21.8 - - + -
64C ASN 3.3 2.4 + - - +
65C MET 3.1 5.0 + - - +
67C ASP* 1.3 78.1 - - - +
69C SER* 1.3 63.0 + - - +
71C TRP* 3.2 4.7 + - - +
72C ILE* 3.0 27.8 + - - +
88C PHE* 3.4 26.2 - - + -
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Residues in contact with SER 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLN* 5.4 0.9 + - - -
65C MET 2.9 14.6 + - - -
66C ARG* 3.4 10.4 - - - -
68C ALA* 1.3 76.2 - - - +
70C GLN* 1.3 60.8 + - - +
72C ILE* 2.8 33.5 + - - +
73C LYS* 3.0 11.7 + - - +
88C PHE* 3.5 14.5 - - - -
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Residues in contact with GLN 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ARG* 2.9 28.2 + - + +
67C ASP* 3.8 7.9 - - - +
69C SER* 1.3 76.7 - - - +
71C TRP* 1.3 62.9 + - - +
73C LYS* 3.2 15.7 + - - +
74C ARG* 3.0 41.9 + - + +
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Residues in contact with TRP 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LEU* 3.4 39.9 - - + -
38C PHE 3.6 24.7 - - - -
39C ALA* 4.3 4.5 - - + -
60C LYS* 3.0 41.3 - - + +
62C PHE* 3.1 34.8 - + + -
67C ASP 2.8 9.4 + - - +
68C ALA 3.3 2.2 - - - +
70C GLN* 1.3 78.3 - - - +
72C ILE* 1.3 67.0 + - + +
74C ARG* 3.4 28.4 + - + +
75C MET* 2.9 64.5 + - + +
82C ALA* 3.5 26.0 - - + -
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Residues in contact with ILE 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 3.5 28.9 - - + -
68C ALA 3.1 14.1 - - - +
69C SER* 2.8 14.6 + - - +
71C TRP* 1.3 83.2 - - + +
73C LYS* 1.3 59.2 + - - +
75C MET* 3.3 3.7 - - - +
76C GLU* 2.6 58.9 + - + +
82C ALA* 4.2 11.2 - - + +
86C ASP* 4.1 28.7 - - + +
88C PHE* 4.8 4.7 - - + -
382C GLN* 5.7 0.9 - - + -
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Residues in contact with LYS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643B ASP* 5.5 12.3 - - + -
644B THR* 5.5 3.4 - - + -
693B LEU 6.1 0.4 - - - +
69C SER 3.0 9.9 + - - +
70C GLN* 3.4 20.2 - - - +
72C ILE* 1.3 77.8 - - - +
74C ARG* 1.3 64.7 + - + +
76C GLU* 3.7 20.8 + - - +
77C ASP* 2.9 34.0 + - - +
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Residues in contact with ARG 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692B PRO* 6.0 4.3 - - + -
693B LEU 5.4 4.3 - - - +
694B GLY 4.1 21.4 + - - +
695B SER* 4.3 17.7 - - - +
62C PHE* 5.5 1.0 - - - -
67C ASP 4.9 1.4 + - - -
70C GLN* 3.0 35.4 + - + +
71C TRP* 3.5 38.5 - - + +
73C LYS* 1.3 77.5 - - + +
75C MET* 1.3 64.2 + - - +
77C ASP* 2.9 19.3 + - - +
78C ILE* 3.1 21.6 + - + +
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Residues in contact with MET 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755B GLU* 6.4 0.2 - - - -
39C ALA* 4.4 9.9 - - + -
71C TRP* 2.9 72.9 + - + +
72C ILE 3.3 6.5 - - - +
74C ARG* 1.3 74.3 - - + +
76C GLU* 1.3 58.2 + - - +
78C ILE* 3.0 22.3 - - - +
79C GLY 3.0 1.9 + - - -
80C LEU* 2.9 52.7 + - + +
81C GLU 3.2 28.5 - - - +
82C ALA* 4.0 7.0 - - + -
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Residues in contact with GLU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721B ALA 5.3 0.5 - - - +
722B GLU* 3.4 12.8 - - - +
72C ILE* 2.6 44.1 + - + +
73C LYS* 3.6 16.3 + - - +
75C MET* 1.3 73.0 - - + +
77C ASP* 1.3 68.2 + - - +
79C GLY* 3.1 8.8 + - - +
80C LEU 4.0 5.1 + - - -
382C GLN* 3.2 40.7 + - - +
383C GLY 5.1 1.0 - - - +
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Residues in contact with ASP 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B THR* 2.9 38.8 - - - +
692B PRO* 3.7 18.3 - - + +
693B LEU 4.3 4.9 + - - +
713B TRP* 3.7 16.0 - - - -
721B ALA 4.7 2.1 - - - +
722B GLU* 4.2 2.6 - - - +
723B PRO* 2.9 24.8 - - - +
73C LYS* 2.9 30.4 + - - +
74C ARG* 3.2 13.3 - - - +
76C GLU* 1.3 79.8 - - - +
78C ILE* 1.3 59.1 + - - +
79C GLY* 3.1 0.5 + - - -
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Residues in contact with ILE 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B PRO* 3.9 17.9 - - + -
722B GLU* 4.7 2.3 - - - +
723B PRO* 4.0 19.7 - - - +
750B ARG* 4.0 1.1 - - - +
754B GLN* 3.6 44.1 + - + +
755B GLU* 3.4 29.4 - - + +
74C ARG* 3.5 12.6 - - + +
75C MET* 3.0 26.9 - - - +
77C ASP* 1.3 73.9 - - - +
79C GLY* 1.3 57.4 + - - +
80C LEU* 3.3 31.6 - - + +
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Residues in contact with GLY 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722B GLU* 3.4 30.1 - - - +
75C MET 3.0 3.6 + - - -
76C GLU* 3.1 4.9 + - - -
77C ASP 3.0 5.3 + - - -
78C ILE* 1.3 79.5 - - - +
80C LEU* 1.3 66.9 + - - +
81C GLU 4.1 0.5 + - - -
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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