Contacts of the strand formed by residues 1126 - 1130 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010B VAL* 4.9 0.4 - - - -
1013B ASN* 2.9 14.3 + - - +
1014B CYS* 3.0 29.6 + - - +
1125B VAL* 1.3 80.0 - - - +
1127B GLU* 1.3 62.4 + - - -
1128B LEU 3.7 0.2 + - - -
1156B ILE* 3.5 11.5 - - - +
1157B ASP 3.7 2.0 - - - -
1158B ALA* 4.3 0.7 - - - -
1161B TYR 3.2 19.1 - - - -
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Residues in contact with GLU1127 (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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1014B CYS* 3.4 8.9 - - - +
1015B VAL* 4.5 0.9 - - - -
1016B THR* 2.7 51.2 + - + +
1126B GLY* 1.3 70.7 - - - -
1128B LEU* 1.3 63.5 + - - +
1129B ILE* 3.5 11.0 + - + +
1137B ARG* 2.9 40.9 + - - -
1156B ILE* 3.4 2.1 - - - -
1157B ASP* 2.8 45.2 + - + +
1160B PHE* 4.1 7.8 - - - +
1161B TYR* 3.8 27.5 + - + -
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Residues in contact with LEU1128 (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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1013B ASN* 5.4 9.6 - - + +
1014B CYS 2.9 17.0 + - - +
1015B VAL* 4.1 13.6 - - + +
1016B THR 4.9 0.7 + - - -
1017B SER 4.7 0.9 - - - +
1019B MET* 3.6 25.9 - - + +
1021B ILE* 3.7 21.8 - - + -
1126B GLY 3.7 2.1 + - - +
1127B GLU* 1.3 72.6 - - - +
1129B ILE* 1.3 63.6 + - - +
1146B LEU* 3.6 19.3 - - + -
1154B TYR* 4.1 4.5 - - + -
1155B CYS 3.4 15.9 - - - +
1156B ILE* 4.6 7.2 - - + +
1190B PHE* 3.3 46.4 - - + -
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Residues in contact with ILE1129 (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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1016B THR* 5.0 1.8 - - - +
1019B MET* 3.9 6.5 - - - -
1127B GLU* 3.6 34.5 - - + +
1128B LEU* 1.3 79.3 - - - +
1130B SER* 1.3 62.6 + - - +
1133B GLU* 4.0 14.6 - - + -
1134B ALA* 3.7 32.3 - - + +
1137B ARG* 3.7 16.8 - - + +
1143B LEU* 4.0 4.9 - - + -
1154B TYR* 3.6 10.9 - - - -
1155B CYS* 2.9 46.1 + - + +
1157B ASP* 3.9 20.2 - - + -
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Residues in contact with SER1130 (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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1019B MET* 3.9 10.2 - - - +
1129B ILE* 1.3 78.8 - - - +
1131B ASP* 1.3 59.6 + - - +
1132B SER* 3.0 23.5 + - - -
1133B GLU* 3.1 14.1 + - - +
1134B ALA* 2.9 28.5 + - - +
1153B VAL 4.9 0.2 - - - -
1154B TYR* 3.8 20.6 - - - -
1155B CYS 4.8 0.4 - - - -
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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