Contacts of the strand formed by residues 61 - 65 (chain A) in PDB entry 1RRM
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 ALA 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLN 3.7 21.3 + - - +
33A LYS* 3.6 18.5 - - + -
34A ALA 3.2 17.5 + - - -
55A MSE 3.8 6.2 - - - +
59A GLY 3.9 2.8 + - - -
60A LEU* 1.3 72.3 - - - +
62A TRP* 1.3 65.8 + - - +
91A TYR* 4.7 0.7 + - - -
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Residues in contact with TRP 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LYS* 4.1 9.3 - - - +
34A ALA* 3.2 13.2 - - + +
36A ILE* 4.3 5.2 - - + -
52A THR* 3.5 31.9 + - + -
55A MSE 4.0 28.3 - - + -
56A ASP* 2.7 33.0 + - - -
60A LEU 3.3 17.9 - - - -
61A ALA* 1.3 75.9 - - - +
63A ALA* 1.3 64.3 + - - +
64A ILE* 3.4 41.5 - - + -
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LYS* 3.9 19.3 - - - +
34A ALA 2.9 6.1 + - - +
35A LEU* 3.4 16.5 - - + -
36A ILE* 2.8 26.3 + - - +
62A TRP* 1.3 76.6 - - - +
64A ILE* 1.3 67.9 + - - +
83A VAL* 6.1 0.9 - - + -
87A SER* 4.3 10.3 - - - -
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 4.2 3.6 - - - -
36A ILE* 3.6 16.4 - - + +
38A THR* 4.0 13.7 - - + -
43A VAL* 4.8 7.6 - - + -
48A VAL* 3.6 28.5 - - + -
52A THR* 4.2 2.0 - - + -
62A TRP* 3.4 34.4 - - + -
63A ALA* 1.3 78.6 - - - +
65A TYR* 1.3 73.0 + - - +
66A ASP* 3.9 13.8 + - + +
83A VAL* 4.5 7.4 - - - +
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Residues in contact with TYR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 4.3 10.5 - - + +
36A ILE 2.8 11.5 + - - +
37A VAL* 4.4 15.0 - - + -
38A THR* 3.0 25.8 + - - +
64A ILE* 1.3 74.5 - - - +
66A ASP* 1.3 60.5 + - - +
67A GLY* 3.7 21.4 + - - -
68A VAL* 4.1 12.1 - - + -
76A VAL* 3.3 31.3 + - + +
79A GLU* 2.8 41.3 + - + +
80A GLY* 3.7 25.6 - - - -
83A VAL* 3.8 29.6 - - + -
103A THR* 4.8 2.9 - - + -
107A ILE* 4.9 2.5 - - + -
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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