Contacts of the strand formed by residues 161 - 166 (chain B) 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 ARG 161 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLU* 2.8 41.8 + - - -
155B THR* 4.5 1.2 - - - +
156B ASP* 2.8 33.2 + - + +
159B LYS* 3.6 37.0 - - + +
160B ARG* 1.3 77.2 - - - +
162B LYS* 1.3 65.9 + - - +
163B PHE* 3.7 15.5 + - - +
268B PRO* 6.1 0.9 - - - -
271B ALA* 3.5 10.8 - - - +
356B ALA* 5.8 9.6 + - + +
359B ASP* 4.9 16.0 + - - +
360B ASP* 5.7 2.4 - - - +
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Residues in contact with LYS 162 (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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71B ASN* 2.8 27.1 - - - +
153B VAL* 3.5 27.5 - - + +
154B ILE 3.4 5.4 - - - -
155B THR* 3.3 25.6 - - - +
161B ARG* 1.3 81.1 + - - +
163B PHE* 1.3 60.3 + - - +
164B VAL* 5.2 0.2 - - - +
267B HIS* 3.5 39.9 + - + +
268B PRO* 5.7 0.6 - - - +
270B GLY* 4.0 8.5 - - - -
271B ALA* 3.5 18.3 - - + +
277B HIS* 5.4 1.2 + - - -
360B ASP* 4.1 14.7 - - - +
389B APR 2.7 34.7 + - - -
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Residues in contact with PHE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 4.1 7.6 - - + -
119B VAL* 3.6 23.1 - - + -
120B ARG* 3.6 22.9 - - + -
123B GLU* 3.3 39.9 - - + +
152B TYR 3.9 0.3 - - - +
153B VAL* 3.4 4.1 - - - -
154B ILE* 2.9 71.6 + - + -
156B ASP* 3.8 33.4 - - + -
161B ARG* 3.8 8.7 - - - +
162B LYS* 1.3 74.9 - - - +
164B VAL* 1.3 61.0 + - - +
165B CYS* 3.6 23.7 + - - -
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Residues in contact with VAL 164 (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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123B GLU* 3.6 5.6 - - - +
124B GLY* 2.8 24.9 + - - -
151B ASN* 4.2 13.5 - - + -
152B TYR 3.7 5.6 - - - +
153B VAL* 4.3 8.1 - - + +
162B LYS 4.2 0.4 + - - +
163B PHE* 1.3 73.1 - - - +
165B CYS* 1.3 70.6 + - - +
166B VAL* 4.2 14.3 - - + +
267B HIS* 3.4 37.2 - - + +
360B ASP* 4.2 7.6 - - - +
361B VAL* 3.7 19.5 - - + +
362B CYS* 4.2 13.7 - - - -
390B PGO 4.4 9.2 - - - +
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Residues in contact with CYS 165 (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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122B LEU* 3.4 39.5 - - - +
123B GLU 3.8 0.2 - - - -
124B GLY 3.7 4.5 - - - -
126B SER* 3.9 2.5 - - - +
150B ILE 3.7 0.7 - - - +
151B ASN* 3.0 7.8 - - - +
152B TYR* 2.8 72.3 + - + +
154B ILE* 5.1 0.7 - - - -
163B PHE* 3.6 27.1 - - - -
164B VAL* 1.3 73.4 - - - +
166B VAL* 1.3 61.7 + - - +
167B ASP 4.1 0.4 - - - -
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Residues in contact with VAL 166 (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 ARG* 5.7 0.4 - - - +
124B GLY 2.8 16.4 + - - +
125B LEU* 3.4 28.0 - - + +
126B SER* 3.2 21.5 + - - +
150B ILE* 3.6 20.9 - - + -
151B ASN* 3.2 24.7 - - - +
164B VAL* 4.2 12.3 - - + +
165B CYS* 1.3 75.6 - - - +
167B ASP* 1.3 62.9 + - - +
168B PRO* 4.6 1.3 - - + +
255B SER 5.4 1.8 - - - +
361B VAL* 4.4 17.0 - - + -
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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