Contacts of the strand formed by residues 1178 - 1184 (chain A) in PDB entry 2ARF
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 THR1178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1037A PRO* 4.6 12.1 - - + +
1174A MET* 5.0 11.5 - - + +
1177A GLN* 1.3 78.1 + - - +
1179A ALA* 1.3 61.0 + - - +
1180A ILE* 4.2 14.0 + - + -
1192A ILE 4.2 0.2 - - - +
1193A ALA* 3.7 0.3 - - - -
1194A ILE* 2.7 74.3 + - + +
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Residues in contact with ALA1179 (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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1149A GLY 5.1 0.7 - - - +
1150A ASN* 4.9 4.5 + - - -
1151A ARG* 5.8 4.5 - - + -
1170A THR* 4.0 26.0 + - + +
1173A GLU* 3.0 38.5 - - + +
1174A MET* 5.5 1.0 - - - +
1177A GLN* 4.0 6.9 + - - +
1178A THR* 1.3 73.1 - - - +
1180A ILE* 1.3 69.0 + - - +
1181A LEU* 5.7 2.5 - - + -
1191A MET* 5.6 7.4 - - + -
1192A ILE 4.1 2.5 - - - -
1193A ALA* 4.9 1.8 - - - +
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Residues in contact with ILE1180 (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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1069A HIS* 4.9 7.4 - - + +
1102A ILE* 6.5 0.4 - - + -
1148A ILE* 4.4 25.8 - - + -
1149A GLY* 4.1 9.0 - - - +
1178A THR* 4.3 15.0 - - + -
1179A ALA* 1.3 80.8 - - - +
1181A LEU* 1.3 62.4 + - - +
1182A VAL* 5.6 0.4 - - + -
1191A MET* 3.3 4.2 - - - +
1192A ILE* 2.7 88.4 + - + +
1194A ILE* 3.5 15.5 - - + -
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Residues in contact with LEU1181 (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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1045A LEU* 3.5 30.3 - - + -
1148A ILE* 3.4 5.2 - - - +
1149A GLY 2.9 39.6 + - - +
1150A ASN 4.7 0.7 - - - +
1151A ARG* 3.3 66.1 - - + +
1154A LEU* 4.5 18.2 - - + +
1155A ARG* 5.2 5.8 - - - +
1159A LEU* 6.6 0.2 - - + -
1179A ALA* 5.7 2.0 - - + -
1180A ILE* 1.3 76.1 - - - +
1182A VAL* 1.3 61.4 + - - +
1183A ALA 4.1 0.4 + - - -
1188A LEU* 5.9 1.1 - - + -
1191A MET* 3.4 30.1 - - + -
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Residues in contact with VAL1182 (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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1045A LEU* 4.5 4.6 - - - +
1060A VAL* 5.9 2.9 - - + -
1146A VAL* 4.2 16.8 - - + -
1147A LEU 3.8 1.6 - - - +
1148A ILE* 3.6 37.7 - - + -
1180A ILE 5.4 1.1 - - - +
1181A LEU* 1.3 73.4 - - - +
1183A ALA* 1.3 60.7 + - - +
1184A ILE* 4.4 0.9 - - + -
1189A CYS* 3.6 20.6 + - - +
1190A GLY 2.5 47.6 + - - +
1191A MET* 3.9 1.8 - - - +
1192A ILE* 4.6 18.2 - - + -
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Residues in contact with ALA1183 (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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1045A LEU* 6.1 1.8 - - + -
1146A VAL* 3.1 6.1 - - - +
1147A LEU* 2.7 41.3 + - + +
1154A LEU* 2.9 40.8 - - + -
1181A LEU 4.1 0.8 - - - -
1182A VAL* 1.3 76.1 - - - +
1184A ILE* 1.3 58.9 + - - +
1186A GLY* 4.3 2.5 - - - -
1187A VAL 3.0 22.2 - - - +
1188A LEU* 4.8 2.9 - - + -
1189A CYS 4.4 0.2 - - - +
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Residues in contact with ILE1184 (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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1050A THR* 5.4 4.7 - - + -
1051A LEU* 6.3 2.0 - - + -
1056A VAL* 4.2 25.6 - - + -
1059A VAL* 6.3 1.1 - - + -
1060A VAL* 4.6 4.9 - - + -
1144A PHE* 6.3 2.7 - - + -
1145A SER 3.8 2.0 - - - +
1146A VAL* 3.3 39.9 - - + -
1182A VAL* 4.4 2.2 - - + -
1183A ALA* 1.3 70.0 - - - +
1185A ASP* 1.3 66.2 + - + +
1187A VAL* 2.5 59.1 + - + +
1189A CYS* 3.2 41.2 - - + +
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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