Contacts of the strand formed by residues 1126 - 1130 (chain A) in PDB entry 2RFI
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 GLY1126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010A VAL* 4.8 1.1 - - - -
1013A ASN* 2.9 13.5 + - - +
1014A CYS* 3.0 28.9 + - - +
1125A VAL* 1.3 81.1 - - - +
1127A GLU* 1.3 63.5 + - - -
1128A LEU 3.7 0.2 + - - -
1156A ILE* 3.4 10.8 - - - +
1157A ASP 3.8 1.6 - - - -
1158A ALA* 4.3 0.2 - - - -
1161A TYR 3.1 20.4 - - - -
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Residues in contact with GLU1127 (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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1014A CYS* 3.4 8.9 - - - +
1015A VAL* 4.6 1.1 - - - -
1016A THR* 2.7 50.7 + - + +
1126A GLY* 1.3 70.6 - - - -
1128A LEU* 1.3 62.3 + - - +
1129A ILE* 3.5 11.8 + - + +
1137A ARG* 2.9 39.1 + - - -
1156A ILE* 3.4 3.1 - - - -
1157A ASP* 2.8 43.3 + - + +
1160A PHE* 4.3 7.8 - - - +
1161A TYR* 3.8 28.0 + - + -
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Residues in contact with LEU1128 (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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1013A ASN* 4.3 22.9 - - + +
1014A CYS 2.8 17.5 + - - +
1015A VAL* 4.0 23.5 - - + +
1016A THR 4.8 0.7 + - - -
1017A SER 4.7 1.0 - - - +
1019A MET* 3.6 23.0 - - + +
1021A ILE* 3.9 28.7 - - + -
1126A GLY 3.7 0.2 + - - -
1127A GLU* 1.3 70.2 - - - +
1129A ILE* 1.3 63.5 - - - +
1146A LEU* 4.1 17.9 - - + -
1154A TYR* 5.8 0.9 - - + -
1155A CYS 3.6 2.9 - - - +
1156A ILE* 3.4 32.8 - - + -
1190A PHE* 4.3 14.8 - - + -
1191A PRO 5.6 0.7 - - - +
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Residues in contact with ILE1129 (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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1016A THR* 5.0 2.0 - - - +
1019A MET* 3.9 10.5 - - + -
1127A GLU* 3.6 34.1 - - + +
1128A LEU* 1.3 80.8 - - - +
1130A SER* 1.3 63.5 + - - +
1133A GLU* 4.0 15.5 - - + -
1134A ALA* 3.6 33.0 - - + +
1137A ARG* 3.7 18.8 - - + +
1143A LEU* 4.1 1.8 - - + -
1154A TYR* 3.3 8.1 - - - +
1155A CYS* 2.8 46.6 + - + +
1157A ASP* 3.9 19.7 - - + -
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Residues in contact with SER1130 (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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1019A MET* 3.9 10.5 - - - +
1129A ILE* 1.3 77.2 - - - +
1131A ASP* 1.3 59.4 + - - +
1132A SER* 3.6 10.4 + - - -
1133A GLU* 3.0 25.5 + - - +
1134A ALA* 2.9 28.9 + - - +
1153A VAL 4.6 1.1 - - - -
1154A TYR* 3.9 18.8 - - - -
1155A CYS 4.8 0.7 - - - -
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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