Contacts of the strand formed by residues 1192 - 1197 (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 ARG1192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1012A GLN* 5.6 9.1 - - - +
1013A ASN* 4.0 16.0 - - - +
1089A VAL* 4.9 5.8 + - + -
1090A GLN* 5.3 2.8 - - - +
1123A GLU* 2.8 43.7 + - - +
1156A ILE* 5.5 0.9 - - - -
1179A VAL 3.3 3.3 - - - +
1180A ARG* 3.4 3.1 - - - -
1181A VAL* 2.9 39.1 + - + +
1182A PHE* 6.1 0.2 - - - +
1183A MET* 3.4 48.6 - - + +
1184A ALA* 4.9 7.1 - - - +
1185A HIS* 5.1 11.4 - - - +
1190A PHE 3.7 5.4 + - - +
1191A PRO* 1.3 76.7 - - - +
1193A ILE* 1.3 60.7 + - - +
1194A ALA 3.7 0.7 + - - -
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Residues in contact with ILE1193 (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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1123A GLU* 3.2 10.2 + - - +
1124A TYR* 2.8 50.5 + - + +
1144A PHE* 3.8 31.0 - - + -
1146A LEU* 3.7 32.5 - - + -
1156A ILE* 4.5 6.2 - - + +
1178A PRO* 3.7 26.7 - - + -
1179A VAL 3.6 2.5 - - - +
1180A ARG* 4.1 24.0 - - + +
1191A PRO* 4.8 2.2 - - + +
1192A ARG* 1.3 76.9 - - - +
1194A ALA* 1.3 60.7 + - - +
1195A PHE* 4.2 4.9 + - + -
9P THR* 4.5 6.3 - - + -
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Residues in contact with ALA1194 (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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1089A VAL* 3.7 24.0 - - + -
1120A PHE* 3.7 20.6 - - + -
1122A CYS 3.8 3.8 - - - -
1123A GLU* 4.4 0.7 - - - +
1177A VAL 3.5 1.6 - - - +
1178A PRO* 3.5 0.8 - - - +
1179A VAL* 2.8 39.3 + - - +
1181A VAL* 3.9 12.6 - - + -
1192A ARG 3.7 0.8 + - - -
1193A ILE* 1.3 73.6 - - - +
1195A PHE* 1.3 61.7 + - - +
1196A PHE* 3.7 11.6 - - + -
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Residues in contact with PHE1195 (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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1120A PHE* 3.6 6.1 - - - -
1121A VAL* 2.9 26.2 + - - -
1122A CYS* 2.8 44.2 + - - +
1124A TYR* 3.7 43.3 - + + -
1144A PHE* 4.2 5.2 - + - -
1165A SER* 3.9 8.5 - - - -
1168A ILE* 4.5 3.4 - - + -
1176A LEU* 4.0 26.5 - - + -
1177A VAL 3.4 3.4 - - - -
1178A PRO* 3.9 24.7 - - + -
1193A ILE* 4.4 2.5 - - + -
1194A ALA* 1.3 70.5 - - - +
1196A PHE* 1.3 61.0 + - - +
1209A PHE* 3.5 52.9 - + - -
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Residues in contact with PHE1196 (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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1053A TYR* 3.8 38.6 - + - -
1057A GLY 4.9 0.9 - - - -
1059A LEU* 3.6 27.8 - - + -
1071A ILE* 4.5 6.5 - - + -
1088A VAL* 4.6 2.0 - - + -
1089A VAL* 3.8 13.5 - - + -
1118A GLY 3.5 13.0 - - - -
1119A THR 3.1 4.5 - - - -
1120A PHE* 3.5 33.0 - + + -
1176A LEU* 3.3 5.3 - - - -
1177A VAL* 2.9 38.9 + - + +
1179A VAL* 3.7 27.8 - - + -
1181A VAL* 4.8 0.4 - - + -
1194A ALA* 3.7 22.2 - - + -
1195A PHE* 1.3 78.3 - - - +
1197A SER* 1.3 65.0 + - - +
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Residues in contact with SER1197 (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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1065A MET* 3.7 6.6 - - - +
1115A ILE* 4.1 8.1 - - - -
1116A PRO 2.8 25.5 + - - -
1117A PRO* 3.5 0.5 - - - +
1118A GLY* 2.8 31.4 + - - -
1119A THR* 2.9 13.9 + - - -
1121A VAL* 4.4 1.6 - - - -
1175A ASN 3.2 7.2 - - - -
1176A LEU* 4.0 4.2 - - - +
1196A PHE* 1.3 74.0 - - - +
1198A THR* 1.3 61.1 + - - +
1199A ARG 3.6 13.2 - - - -
1201A ILE* 3.7 19.7 - - - -
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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