Contacts of the strand formed by residues 1137 - 1141 (chain A) in PDB entry 6TPG
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 ILE1137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113A ASP 3.3 11.8 + - - +
1114A PHE* 3.1 43.2 - - + +
1115A VAL* 2.9 22.9 + - - -
1135A GLY 4.2 8.1 - - - +
1136A ALA* 1.3 73.9 - - - +
1138A PRO* 1.3 72.3 - - + +
1139A ILE* 5.4 1.1 - - + -
1155A GLY* 4.5 1.1 - - - -
1156A ILE* 5.3 2.7 - - + +
1176A LEU* 6.5 0.7 - - + -
1181A LEU* 4.0 26.5 - - + -
1184A PHE* 3.0 58.8 - - + -
1185A ARG* 4.3 7.2 - - + -
1188A CYS* 4.4 2.0 - - - -
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Residues in contact with PRO1138 (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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1115A VAL* 3.3 19.7 - - + +
1117A ILE* 4.4 10.5 - - + -
1128A ALA* 4.9 2.5 - - + -
1132A MET* 3.9 24.9 - - + -
1136A ALA 3.5 9.6 - - - +
1137A ILE* 1.3 87.2 - - + +
1139A ILE* 1.3 62.0 + - - +
1140A ALA* 3.8 0.9 - - + -
1150A ILE* 3.9 23.0 - - + +
1154A THR 3.6 25.4 - - - +
1155A GLY* 3.5 1.6 - - - -
1156A ILE 3.1 23.9 + - - +
1188A CYS* 4.0 2.2 - - - -
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Residues in contact with ILE1139 (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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1035A PHE* 3.8 34.3 - - + -
1114A PHE* 4.1 13.7 - - + -
1115A VAL 2.8 10.8 + - - +
1116A ILE* 3.4 10.9 - - + +
1117A ILE 2.9 23.8 + - - -
1138A PRO* 1.3 74.8 - - - +
1140A ALA* 1.3 59.7 + - - +
1156A ILE* 3.4 22.0 - - + +
1158A VAL* 4.4 3.6 - - + -
1166A LEU* 3.9 25.0 - - + +
1169A ALA* 3.9 22.0 - - + +
1170A ILE* 4.3 10.5 - - + -
1173A ALA* 3.8 16.4 - - + -
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Residues in contact with ALA1140 (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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1117A ILE* 3.3 16.8 - - + +
1118A PRO* 5.3 0.2 - - - -
1138A PRO 3.8 0.6 - - - -
1139A ILE* 1.3 77.6 - - - +
1141A SER* 1.3 63.6 + - - +
1146A LEU* 3.7 19.7 - - + -
1150A ILE* 3.4 30.3 - - + -
1156A ILE 3.0 6.9 + - - -
1157A LEU* 3.2 7.0 - - + -
1158A VAL* 3.0 28.7 + - - +
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Residues in contact with SER1141 (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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1117A ILE 3.1 8.8 + - - -
1118A PRO* 3.3 18.0 + - - +
1119A SER 2.6 29.8 + - - -
1140A ALA* 1.3 74.3 - - - +
1142A ALA* 1.3 60.4 + - - +
1143A VAL* 2.9 15.0 + - - -
1146A LEU* 3.3 21.1 - - - +
1157A LEU* 3.9 1.6 - - - +
1158A VAL* 3.2 12.9 - - - +
1160A ALA* 3.7 21.8 - - - -
1161A GLY 4.6 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