Contacts of the helix formed by residues 87 - 97 (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 ASP 87 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLN* 5.4 0.5 - - - +
85B MET* 3.2 29.1 - - - +
86B ASP* 1.3 82.4 + - - +
88B PHE* 1.3 61.9 + - - +
89B LYS* 3.5 33.4 + - - +
90B LEU* 3.2 27.6 + - + +
91B ALA 3.3 0.3 + - - -
363B LYS* 2.9 39.1 + - - +
366B ASP* 5.8 0.9 - - - +
576B ARG* 5.9 0.4 - - - +
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Residues in contact with PHE 88 (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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10B GLN* 4.0 17.0 + - - +
15B ILE* 4.8 1.3 - - - -
33B TYR* 3.9 5.8 - + + -
35B PRO* 3.4 29.4 - - + -
36B SER 5.3 0.4 - - - -
37B LEU* 4.5 13.2 - - + -
65B MET* 3.5 48.7 - - + -
68B ALA* 3.5 22.4 - - + -
69B SER* 4.2 15.7 - - - -
72B ILE* 4.9 2.7 - - + -
85B MET 3.9 17.9 - - - -
86B ASP* 3.4 16.7 + - - -
87B ASP* 1.3 70.4 + - - +
89B LYS* 1.3 56.6 + - - +
91B ALA* 3.0 7.3 + - + +
92B TYR* 2.7 37.5 + - - +
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Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 3.9 30.8 - - + +
9B GLU* 4.2 16.8 + - - +
10B GLN* 4.3 22.5 + - + +
15B ILE* 4.4 9.5 - - + +
87B ASP* 3.3 20.6 + - - +
88B PHE* 1.3 76.0 - - - +
90B LEU* 1.3 64.6 + - + +
92B TYR* 3.3 4.2 + - - +
93B LEU* 2.9 33.3 + - - +
354B GLN* 3.6 34.5 + - + +
363B LYS* 6.0 1.6 - - - +
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B MET* 3.6 28.3 - - + -
87B ASP* 3.2 34.6 + - + +
89B LYS* 1.3 87.6 - - + +
91B ALA* 1.3 56.4 + - - +
93B LEU* 3.8 7.4 - - + +
94B SER* 3.0 27.4 + - - -
352B LYS* 4.2 11.4 - - - +
353B ILE* 4.2 24.0 - - + -
354B GLN* 4.8 7.6 - - + +
363B LYS* 4.4 20.6 - - + +
366B ASP* 5.0 2.5 - - - +
367B ALA* 4.1 21.3 - - + +
370B PHE* 3.8 4.9 - - + -
371B ASN* 5.7 0.3 + - - -
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Residues in contact with ALA 91 (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 TYR* 3.4 19.3 - - + +
35B PRO* 5.8 0.4 - - + -
85B MET* 4.2 15.0 - - + +
87B ASP 3.3 4.8 + - - +
88B PHE* 3.0 17.8 + - + +
90B LEU* 1.3 76.3 - - - +
92B TYR* 1.3 60.2 + - - +
94B SER* 3.1 3.6 + - - -
95B ASP* 2.8 33.4 + - - -
370B PHE* 4.0 16.8 - - + -
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Residues in contact with TYR 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 4.1 3.8 - - + -
15B ILE* 3.9 39.3 - - + -
17B GLU* 2.3 40.4 + - + +
29B ARG* 3.5 19.8 + - - -
31B VAL* 3.9 23.3 - - + +
33B TYR* 3.6 37.8 + + + -
88B PHE 2.7 20.6 + - - +
89B LYS* 3.6 4.0 - - - +
91B ALA* 1.3 73.6 - - - +
93B LEU* 1.3 70.3 + - + +
95B ASP* 3.4 1.1 + - - +
96B THR* 2.8 56.1 + - + -
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Residues in contact with LEU 93 (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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5B TYR* 3.6 58.6 - - + +
8B VAL* 3.7 34.8 - - + -
17B GLU* 4.9 0.4 - - - +
89B LYS 2.9 15.1 + - - +
90B LEU* 3.8 6.3 - - + +
92B TYR* 1.3 87.6 - - + +
94B SER* 1.3 55.0 + - - +
97B TYR* 2.8 47.2 + - + +
352B LYS* 3.6 24.0 - - + +
353B ILE* 4.0 7.2 - - - +
354B GLN 4.7 0.4 - - - +
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Residues in contact with SER 94 (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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90B LEU 3.0 19.7 + - - -
91B ALA 3.1 4.9 + - - -
93B LEU* 1.3 78.6 - - - +
95B ASP* 1.3 60.5 + - - +
97B TYR 3.5 1.9 - - - +
98B ASN* 3.5 19.9 + - - +
352B LYS* 4.4 8.6 + - - +
370B PHE* 3.6 12.5 - - - -
371B ASN* 2.9 28.9 + - - -
374B LYS* 2.6 37.5 + - - +
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Residues in contact with ASP 95 (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 TYR* 2.5 36.5 + - + +
91B ALA* 2.8 12.0 + - - +
92B TYR* 3.7 4.3 - - - +
94B SER* 1.3 78.1 - - - +
96B THR* 1.3 63.6 + - - +
97B TYR 3.3 0.5 + - - -
98B ASN* 3.9 12.8 + - - +
370B PHE* 5.9 0.5 - - - -
374B LYS* 2.7 33.4 + - - +
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Residues in contact with THR 96 (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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17B GLU* 4.2 3.1 - - - +
29B ARG* 4.0 18.8 - - - +
92B TYR* 2.8 49.2 + - - -
95B ASP* 1.3 73.7 - - - +
97B TYR* 1.3 97.5 + - + +
98B ASN 3.8 0.8 + - - -
99B TYR* 4.6 4.3 + - - -
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Residues in contact with TYR 97 (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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3B GLU* 3.6 26.2 + - + +
4B PHE* 3.6 5.8 + - - -
5B TYR* 3.4 40.5 + + + -
17B GLU* 2.5 30.4 + - - -
19B TYR* 3.6 13.5 - - - +
29B ARG* 4.3 2.6 + - - -
93B LEU* 2.8 22.7 + - + +
94B SER 3.5 3.8 - - - -
96B THR* 1.3 105.4 - - + +
98B ASN* 1.3 49.5 + - - +
99B TYR* 2.9 34.2 + + - +
101B ILE* 3.4 22.2 - - + -
352B LYS* 2.6 35.9 + - + -
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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