Contacts of the strand formed by residues 151 - 156 (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 ASN 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ASP* 3.9 3.8 - - - +
105A LYS* 2.9 22.3 + - - +
146A ALA* 5.4 0.3 - - - -
149A THR* 3.3 5.7 + - - -
150A ILE* 1.3 104.7 + - - +
152A TYR* 1.3 64.8 + - - +
164A VAL* 4.3 11.6 - - + +
165A CYS 3.0 9.0 - - - +
166A VAL* 3.5 24.1 - - - +
254A PHE* 4.3 9.0 - - - +
255A SER* 4.5 10.0 + - - +
259A LEU* 5.9 0.3 - - - +
390A PGO 3.3 33.5 - - + +
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Residues in contact with TYR 152 (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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102A ASP* 3.4 39.5 - - + +
105A LYS* 3.7 16.2 - - + -
106A ALA* 3.8 21.2 - - + -
109A ILE* 3.3 29.1 - - + +
119A VAL* 6.1 0.2 - - + -
122A LEU* 3.4 29.4 - - + +
126A SER* 4.5 0.9 + - - -
151A ASN* 1.3 78.8 - - - +
153A VAL* 1.3 60.2 + - - +
154A ILE* 4.1 11.9 - - + -
163A PHE 3.9 0.5 - - - +
164A VAL* 4.6 1.1 - - - -
165A CYS* 2.8 59.4 + - + +
167A ASP* 5.0 1.6 - - + -
170A ASP* 3.2 28.5 - - + -
390A PGO 5.5 2.7 - - - -
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Residues in contact with VAL 153 (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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71A ASN 5.5 0.2 - - - -
72A PRO* 3.7 15.6 - - - +
102A ASP* 2.9 17.4 + - - +
152A TYR* 1.3 74.2 - - - +
154A ILE* 1.3 71.0 + - - +
162A LYS* 3.7 39.0 + - + +
163A PHE 3.4 16.4 - - - +
164A VAL* 4.3 15.3 - - + +
267A HIS* 4.7 4.7 - - + +
389A APR 3.1 33.2 + - - +
390A PGO 4.6 10.3 - - - +
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Residues in contact with ILE 154 (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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72A PRO* 3.4 21.1 - - + +
73A THR 3.6 20.9 - - - +
74A ILE* 3.6 8.7 - - + +
77A VAL* 3.8 23.1 - - + -
102A ASP 4.1 20.4 - - - +
106A ALA* 4.2 2.5 - - + -
119A VAL* 4.3 5.4 - - + -
152A TYR* 4.1 17.7 - - + -
153A VAL* 1.3 82.5 - - - +
155A THR* 1.3 65.2 + - - +
162A LYS* 3.3 2.2 - - - -
163A PHE* 2.8 64.5 + - + -
165A CYS* 5.0 0.2 - - - -
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Residues in contact with THR 155 (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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71A ASN* 3.1 28.6 + - + +
72A PRO 2.7 16.4 + - - -
73A THR* 3.3 12.9 - - + -
74A ILE* 3.1 24.4 + - - +
154A ILE* 1.3 72.2 - - - +
156A ASP* 1.3 69.0 + - - +
157A GLU* 3.4 13.0 + - + +
160A ARG* 5.7 0.7 - - - -
161A ARG 3.7 10.3 - - - +
162A LYS* 3.5 21.2 + - + +
163A PHE* 4.2 2.0 - - - -
270A GLY 5.4 0.8 + - - +
271A ALA* 4.8 13.5 - - - +
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Residues in contact with ASP 156 (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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74A ILE* 3.7 13.0 - - - +
120A ARG* 2.8 50.3 + - - +
154A ILE 3.8 1.2 + - - -
155A THR* 1.3 71.2 - - - +
157A GLU* 1.3 51.9 + - - +
158A GLU* 3.2 4.3 + - - +
159A LYS* 3.2 28.8 + - - +
160A ARG 2.8 30.3 + - - -
161A ARG* 2.7 30.1 + - + +
163A PHE* 3.8 14.0 - - + -
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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