Contacts of the strand formed by residues 135 - 139 (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 ILE 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.4 15.7 - - + +
94A ALA* 4.5 6.7 - - + -
104A CYS* 3.9 22.4 - - + +
105A LYS* 3.8 37.5 - - + +
132A SER* 3.7 17.0 - - - +
133A VAL 3.3 12.8 + - - +
134A PRO* 1.3 74.9 - - - +
136A LEU* 1.3 76.3 - - - +
137A ALA* 4.2 1.8 - - + +
170A ASP 4.2 9.2 - - - +
171A ILE 5.5 0.8 + - - +
172A PRO* 3.5 23.8 - - + +
173A GLN* 2.8 33.7 + - - +
174A VAL 3.6 2.4 + - - -
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Residues in contact with LEU 136 (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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22A LEU* 4.2 11.4 - - + +
25A GLU* 4.9 3.1 - - + -
26A VAL* 3.6 35.0 - - + +
29A ARG* 5.0 0.7 - - - -
31A TYR* 4.0 24.0 - - + +
91A TYR* 4.0 13.0 - - + -
92A LEU 2.8 11.2 + - - +
93A ILE* 3.2 12.5 - - + +
94A ALA 3.0 22.7 + - - -
135A ILE* 1.3 83.1 - - - +
137A ALA* 1.3 60.6 + - - +
138A ILE* 4.9 0.2 - - - -
173A GLN* 4.7 5.4 - - + -
174A VAL* 3.4 21.5 - - + -
176A PHE* 4.0 28.0 - - + -
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Residues in contact with ALA 137 (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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94A ALA* 3.9 7.0 - - + +
101A GLN* 3.5 21.8 - - - +
135A ILE* 3.9 5.1 - - + -
136A LEU* 1.3 71.0 - - - +
138A ILE* 1.3 65.2 + - - +
139A PRO* 3.7 3.3 - - - +
147A GLU* 3.6 19.7 - - + +
172A PRO* 4.1 16.4 - - + -
174A VAL 2.9 11.7 + - - +
175A ALA* 3.4 0.7 - - - -
176A PHE* 2.9 28.8 + - - -
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Residues in contact with ILE 138 (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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19A VAL* 3.8 20.9 - - + -
22A LEU* 3.6 27.8 - - + -
51A VAL* 4.1 19.7 - - + -
93A ILE* 3.8 18.4 - - + -
94A ALA 2.8 15.6 + - - +
95A ILE* 3.5 5.1 - - + -
96A GLY 3.1 21.2 + - - -
101A GLN* 4.7 1.1 - - - -
136A LEU 4.6 0.4 - - - +
137A ALA* 1.3 80.0 - - - +
139A PRO* 1.3 63.9 - - - +
140A THR* 3.9 1.4 - - - +
176A PHE* 3.7 20.0 - - + +
181A MSE 3.7 31.6 - - + -
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Residues in contact with PRO 139 (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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96A GLY 3.2 9.0 - - - +
101A GLN* 3.4 16.4 - - - +
137A ALA 3.7 5.6 - - - +
138A ILE* 1.3 88.9 - - - +
140A THR* 1.3 61.9 + - - +
141A THR* 3.6 13.9 - - - +
147A GLU* 3.5 35.7 - - + +
176A PHE 3.2 18.9 - - - +
177A ILE* 4.4 4.7 - - + -
178A ASP 4.6 1.0 + - - +
181A MSE 3.8 12.6 - - - +
182A MSE 3.8 22.8 - - + +
247A GLN* 5.0 1.1 - - - +
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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