Contacts of the strand formed by residues 91 - 96 (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 TYR 91 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 3.4 34.7 - - + +
31A TYR* 3.2 50.3 - + + -
32A GLN 4.8 0.4 - - - -
33A LYS* 3.3 10.4 - - - +
34A ALA* 3.1 41.1 + - + +
35A LEU 3.1 21.8 + - - -
55A MSE 3.4 18.9 - - - +
60A LEU* 5.1 0.7 - - - +
61A ALA 4.7 0.7 + - - -
84A PHE* 4.0 2.6 - - - -
89A ALA* 3.6 5.1 - - - +
90A ASP* 1.3 89.6 - - - +
92A LEU* 1.3 73.2 + - - +
93A ILE* 3.6 13.5 - - + -
133A VAL* 3.8 5.6 - - - +
134A PRO* 3.6 13.7 - - + +
136A LEU* 4.0 9.6 - - + -
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Residues in contact with LEU 92 (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* 3.5 12.8 - - + +
37A VAL* 3.8 24.9 - - + -
84A PHE* 3.6 28.3 - - + -
91A TYR* 1.3 78.8 - - - +
93A ILE* 1.3 65.7 + - - +
94A ALA 4.1 0.7 - - - -
104A CYS* 3.5 21.8 - - - +
107A ILE* 4.3 8.5 - - + -
108A GLY* 3.6 35.4 - - - +
133A VAL* 4.0 12.3 - - + -
134A PRO 2.8 10.0 + - - +
135A ILE* 3.4 10.5 - - + -
136A LEU* 2.8 26.9 + - - +
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Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.4 13.0 - - + -
34A ALA* 3.5 23.3 - - + -
35A LEU 3.0 6.8 + - - +
36A ILE* 3.2 14.3 - - + +
37A VAL 2.8 25.4 + - - -
51A VAL* 5.0 0.9 - - + -
55A MSE 3.7 29.8 - - + -
91A TYR* 3.6 23.1 - - + +
92A LEU* 1.3 72.5 - - - +
94A ALA* 1.3 61.1 + - - +
95A ILE* 3.6 16.7 + - + -
104A CYS* 4.6 1.6 - - - -
136A LEU* 3.2 12.6 - - + +
138A ILE* 3.8 28.5 - - + -
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Residues in contact with ALA 94 (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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37A VAL 3.6 5.4 - - - -
92A LEU 4.1 1.4 - - - -
93A ILE* 1.3 71.6 - - - +
95A ILE* 1.3 59.9 + - - +
96A GLY 4.0 0.2 - - - -
100A PRO 4.4 1.8 - - - +
101A GLN* 4.0 25.0 - - + +
104A CYS* 3.8 30.2 - - + -
135A ILE* 4.5 7.4 - - + -
136A LEU 3.0 10.4 + - - +
137A ALA* 4.5 4.0 - - + -
138A ILE* 2.8 33.3 + - - +
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Residues in contact with ILE 95 (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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36A ILE* 3.6 27.6 - - + -
37A VAL 3.0 9.4 + - - -
38A THR* 2.8 44.3 + - - +
42A LEU* 3.4 2.0 - - + +
47A VAL* 4.3 7.6 - - + -
48A VAL* 4.3 15.5 - - + -
51A VAL* 3.8 33.9 - - + -
93A ILE* 3.6 14.3 + - + -
94A ALA* 1.3 75.7 - - - +
96A GLY* 1.3 59.8 + - - +
100A PRO* 3.8 3.2 - - - +
138A ILE* 3.5 11.4 - - + +
140A THR* 4.1 7.9 - - + -
181A MSE 4.0 22.4 - - + -
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Residues in contact with GLY 96 (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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42A LEU* 3.3 11.2 - - - -
94A ALA 4.0 1.4 - - - -
95A ILE* 1.3 76.8 - - - +
97A GLY* 1.3 63.3 + - - -
100A PRO* 4.1 4.7 - - - +
101A GLN* 3.2 18.8 + - - +
138A ILE 3.1 8.5 + - - -
139A PRO* 3.2 1.0 - - - +
140A THR* 3.0 34.2 + - - +
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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