Contacts of the strand formed by residues 1142 - 1151 (chain A) in PDB entry 1SIW
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 GLY1142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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725A GLU* 4.1 4.9 - - - -
737A GLY 3.4 20.9 - - - -
739A GLN* 4.4 2.7 - - - -
1138A PHE* 3.3 2.5 - - - +
1139A ASN* 3.1 31.4 + - - +
1140A SER 3.3 1.2 + - - -
1141A ASN* 1.3 79.5 - - - +
1143A ALA* 1.3 60.7 + - - -
1186A SER 3.0 10.9 + - - -
1187A VAL* 3.5 4.3 - - - +
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Residues in contact with ALA1143 (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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725A GLU* 4.7 2.6 + - - +
737A GLY 4.5 2.4 + - - -
1136A GLU* 3.9 19.1 - - - +
1137A VAL 3.3 4.9 - - - +
1138A PHE* 3.3 20.2 - - + -
1142A GLY* 1.3 73.8 - - - -
1144A LEU* 1.3 61.4 + - - +
1174A SER* 4.5 1.9 - - - +
1176A ILE* 4.2 14.8 - - + -
1177A THR* 4.4 12.4 - - + +
1181A GLY* 5.6 0.2 - - - -
1182A GLY* 3.1 23.8 + - - -
1186A SER* 3.5 11.2 + - - -
1187A VAL* 4.2 1.3 - - - -
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Residues in contact with LEU1144 (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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1088A PHE* 4.0 13.2 - - + -
1117A VAL* 4.5 0.9 - - + -
1136A GLU* 3.5 6.9 - - - +
1137A VAL* 2.8 60.6 + - + +
1143A ALA* 1.3 74.7 - - - +
1145A THR* 1.3 76.2 + - - +
1146A ALA* 4.3 7.0 - - + +
1161A MET* 3.8 31.6 - - + -
1182A GLY 3.4 21.3 - - - +
1183A ILE* 3.5 23.1 - - - +
1184A HIS* 3.8 6.1 - - - -
1187A VAL* 4.3 9.6 - - + -
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Residues in contact with THR1145 (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 PRO* 4.5 0.9 - - - +
1134A TRP* 5.0 0.4 - - - -
1135A ILE 3.6 3.8 - - - -
1136A GLU* 4.0 7.0 - - - +
1144A LEU* 1.3 81.1 - - - +
1146A ALA* 1.3 64.7 + - - +
1161A MET* 5.1 1.2 - - - +
1171A LEU* 3.1 24.2 - - - +
1172A PRO* 3.4 29.1 + - - +
1173A GLY 4.0 3.6 - - - +
1174A SER* 3.9 28.3 - - - -
1181A GLY* 3.5 13.8 - - - -
1182A GLY 4.0 5.2 + - - +
1227A MET* 3.9 25.8 - - + -
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Residues in contact with ALA1146 (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 PRO* 3.6 17.0 - - - +
1116A VAL* 3.9 3.8 - - - -
1117A VAL* 3.8 28.7 - - + -
1134A TRP* 3.4 16.3 - - - -
1135A ILE* 2.8 36.3 + - + -
1144A LEU* 4.3 5.8 - - + +
1145A THR* 1.3 78.8 - - - +
1147A ARG* 1.3 63.0 + - - +
1161A MET* 4.4 4.3 - - + -
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Residues in contact with ARG1147 (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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1112A ARG* 2.7 30.3 + - - +
1113A GLY* 3.4 21.2 + - - -
1114A GLY* 3.4 15.4 + - - +
1115A PRO* 3.2 6.5 + - - +
1116A VAL* 3.0 18.8 - - + +
1117A VAL 2.9 23.1 + - - -
1132A ASN* 2.9 44.3 + - - +
1133A ASP 3.3 3.4 - - - +
1134A TRP* 3.5 47.1 - - + -
1135A ILE* 4.6 2.0 - - - -
1146A ALA* 1.3 75.2 - - - +
1148A ALA* 1.3 59.9 + - - +
1170A ASN* 3.6 10.5 + - - +
137B LYS* 3.9 16.2 - - - -
138B ILE* 3.9 13.9 + - - +
144B TRP* 4.0 3.4 - - - -
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Residues in contact with ALA1148 (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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1112A ARG* 3.9 2.4 + - - -
1117A VAL* 3.4 6.7 - - - +
1119A LEU* 4.3 12.3 - - + -
1129A ILE* 3.7 30.5 - - + -
1130A ALA 4.2 5.6 - - - +
1131A ASP* 3.7 0.7 - - - +
1132A ASN* 2.8 28.7 + - - +
1133A ASP 3.0 14.3 + - - +
1135A ILE* 4.1 10.7 - - + +
1146A ALA 4.2 0.4 + - - -
1147A ARG* 1.3 75.2 - - - +
1149A VAL* 1.3 65.8 + - - +
1150A VAL* 4.7 1.6 - - + -
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Residues in contact with VAL1149 (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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1112A ARG* 4.0 26.5 - - + +
1116A VAL* 3.8 31.9 - - + -
1117A VAL 2.8 10.1 + - - +
1118A TRP* 3.3 49.0 - - + +
1119A LEU* 2.9 25.1 + - - -
1131A ASP* 3.3 3.8 - - - -
1148A ALA* 1.3 78.3 - - - +
1150A VAL* 1.3 60.7 + - - +
1151A SER 3.8 0.5 + - - -
149B GLY* 4.0 14.8 - - - -
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Residues in contact with VAL1150 (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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1119A LEU* 3.5 4.0 - - + +
1121A GLU* 3.6 29.4 - - + +
1124A ALA* 3.7 24.0 - - + -
1129A ILE* 4.1 6.5 - - + +
1130A ALA* 4.0 6.3 - - - +
1131A ASP* 2.8 38.0 + - + +
1148A ALA* 4.7 2.9 - - + -
1149A VAL* 1.3 73.2 - - - +
1151A SER* 1.3 65.6 + - - +
150B GLY* 2.8 31.9 + - - -
151B GLU* 3.7 27.6 - - + +
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Residues in contact with SER1151 (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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1118A TRP* 3.7 24.9 - - - -
1119A LEU 2.9 8.3 + - - +
1120A SER* 3.3 24.6 - - - -
1121A GLU* 3.4 7.3 + - - -
1149A VAL 3.8 0.2 + - - -
1150A VAL* 1.3 76.1 - - - +
1152A GLN* 1.3 63.9 + - - +
1153A ARG* 3.2 22.5 + - - +
1154A VAL* 3.5 8.1 + - - -
148B LEU* 2.7 28.6 + - - +
150B GLY 4.1 2.7 - - - -
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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