Contacts of the strand formed by residues 1176 - 1182 (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 LEU1176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1121A VAL* 3.7 34.8 - - + -
1168A ILE* 3.9 24.9 - - + -
1174A PRO* 3.6 15.6 - - - +
1175A ASN* 1.3 95.5 - - - +
1177A VAL* 1.3 60.5 + - - +
1178A PRO* 4.5 0.3 - - - +
1195A PHE* 4.0 18.6 - - + -
1196A PHE 3.3 12.1 - - - +
1197A SER* 4.0 1.3 - - - -
1198A THR* 3.7 3.8 - - - +
1201A ILE* 4.0 8.1 - - + -
1207A LEU* 3.8 26.7 - - + -
1208A GLY 3.0 13.0 + - - +
1209A PHE* 3.5 20.1 - - + +
1210A ASP 4.7 0.2 + - - -
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Residues in contact with VAL1177 (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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1063A PHE* 5.3 2.0 - - + -
1065A MET* 3.5 51.4 - - + +
1068A PRO* 4.1 7.4 - - + -
1174A PRO* 6.3 0.2 - - + -
1176A LEU* 1.3 75.4 - - - +
1178A PRO* 1.3 83.2 - - + +
1179A VAL* 4.0 12.9 - - + +
1194A ALA 3.5 0.9 - - - +
1195A PHE* 3.4 4.5 - - - -
1196A PHE* 2.9 41.9 + - + +
1198A THR* 3.8 7.6 - - + -
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Residues in contact with PRO1178 (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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1068A PRO* 4.1 8.0 - - - +
1144A PHE* 3.9 19.5 - - + -
1176A LEU 4.5 1.6 - - - +
1177A VAL* 1.3 94.9 - - + +
1179A VAL* 1.3 62.6 + - - +
1193A ILE* 3.7 23.6 - - + -
1194A ALA 3.5 5.8 - - - +
1195A PHE* 3.9 10.8 - - + -
1209A PHE* 4.3 21.5 - - + -
1210A ASP 5.3 3.1 - - - +
8P SER 4.5 1.6 - - - +
9P THR* 4.2 28.0 - - + +
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Residues in contact with VAL1179 (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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1063A PHE* 4.0 22.2 - - + -
1068A PRO* 4.1 9.9 - - + -
1069A PRO 3.8 17.7 - - - +
1071A ILE* 3.8 27.8 - - + -
1177A VAL* 4.0 11.7 - - + +
1178A PRO* 1.3 80.7 - - - +
1180A ARG* 1.3 69.8 + - - +
1181A VAL* 3.7 3.6 + - + +
1192A ARG 3.3 2.8 - - - +
1193A ILE* 3.6 3.7 - - - -
1194A ALA 2.8 36.7 + - - +
1196A PHE* 3.7 25.4 - - + -
9P THR* 5.6 0.2 - - - -
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Residues in contact with ARG1180 (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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1068A PRO* 5.7 2.0 + - - +
1069A PRO 4.8 1.4 + - - +
1070A LEU* 3.6 32.3 - - + +
1071A ILE 3.0 23.4 + - - -
1145A ASP 4.7 1.0 + - - -
1146A LEU* 2.9 33.5 + - - +
1147A ASP* 4.1 6.6 - - - +
1148A ASN* 4.0 14.3 + - - +
1179A VAL* 1.3 74.2 - - - +
1181A VAL* 1.3 61.9 + - - +
1182A PHE* 4.9 1.1 - - - -
1191A PRO* 3.7 22.4 - - + -
1192A ARG 3.4 4.9 - - - -
1193A ILE* 4.1 12.1 - - + +
9P THR* 2.5 44.3 + - + +
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Residues in contact with VAL1181 (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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1071A ILE* 3.3 24.0 - - + +
1073A GLU* 4.0 22.9 - - + +
1089A VAL* 4.2 8.1 - - + -
1179A VAL* 3.7 17.9 - - + +
1180A ARG* 1.3 80.1 - - - +
1182A PHE* 1.3 75.8 + - - +
1183A MET* 3.7 23.9 - - + +
1190A PHE 5.0 0.2 - - - +
1191A PRO* 3.9 1.1 - - - +
1192A ARG* 2.9 38.0 + - - +
1194A ALA* 3.9 20.0 - - + -
1196A PHE* 4.8 0.4 - - + -
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Residues in contact with PHE1182 (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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1070A LEU* 4.2 23.3 - - + -
1071A ILE 2.8 13.1 + - - -
1072A PHE* 3.7 38.5 - + + -
1073A GLU* 2.9 28.6 + - - +
1181A VAL* 1.3 78.3 - - - +
1183A MET* 1.3 65.4 + - - +
1185A HIS* 3.6 22.9 - + - +
1186A GLN* 4.0 9.4 - - + -
1187A ASP 3.3 24.0 - - - -
1188A LEU* 3.7 32.3 - - + -
1190A PHE 4.0 0.9 - - - -
1191A PRO* 3.6 33.2 - - + -
1192A ARG* 6.1 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