Contacts of the helix formed by residues 1132 - 1140 (chain B) in PDB entry 1B0P
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 ASN1132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1188A PHE 3.0 20.0 - - - +
1190A GLU 3.0 19.6 + - - +
1191A GLY 4.1 4.8 + - - -
1192A ALA* 3.6 21.7 - - + +
1193A GLU* 5.7 0.9 - - - +
1074B GLN 3.2 1.0 + - - -
1075B GLY* 2.8 28.2 + - - +
1077B ARG* 4.1 5.2 - - - +
1131B GLN* 1.3 68.0 - - - +
1133B ARG* 1.3 59.3 + - - +
1134B PHE 3.0 5.6 - - - -
1135B ALA* 3.7 2.9 - - - -
1136B VAL* 2.7 34.7 + - - +
1139B ARG* 2.7 42.2 - - - +
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Residues in contact with ARG1133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188A PHE* 4.6 6.0 + - + -
991B THR 4.7 0.2 + - - -
992B GLU* 2.8 40.8 + - - +
1006B PRO* 3.9 11.7 - - - +
1008B GLY 4.2 0.2 - - - +
1009B ALA* 3.8 7.3 - - - +
1010B VAL* 2.9 53.7 + - - +
1068B TYR* 2.9 23.8 + - - -
1073B ASN 4.5 4.5 - - - +
1074B GLN* 3.1 46.7 + - - +
1095B TYR* 3.6 9.7 + - - -
1131B GLN* 2.8 27.9 + - + +
1132B ASN* 1.3 77.9 - - - +
1134B PHE* 1.3 81.7 + - + +
1136B VAL* 4.1 4.0 - - - -
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Residues in contact with PHE1134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006B PRO* 3.7 22.4 - - + -
1007B THR 4.0 10.5 - - - -
1008B GLY* 3.7 14.8 - - - -
1009B ALA* 3.7 25.4 - - + -
1095B TYR* 3.8 6.3 - + - -
1128B LEU* 3.2 66.6 - - + +
1129B MET* 4.0 10.5 - - + +
1131B GLN* 3.3 9.3 + - + -
1132B ASN 3.0 0.2 - - - -
1133B ARG* 1.3 111.7 - - + +
1135B ALA* 1.3 64.0 + - - +
1136B VAL 3.3 1.8 - - - -
1137B LEU* 3.3 18.2 + - - +
1138B ASP 3.6 4.0 + - - -
1145B ALA* 5.1 0.2 - - - +
1149B ARG* 4.8 8.7 + - + +
1152B VAL* 5.3 1.1 - - + -
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Residues in contact with ALA1135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077B ARG* 3.7 17.5 - - - +
1129B MET* 3.8 27.1 - - - +
1131B GLN 2.9 17.1 + - - +
1132B ASN* 3.4 2.4 + - - -
1134B PHE* 1.3 76.9 - - - +
1136B VAL* 1.3 65.2 + - - +
1137B LEU 3.2 0.2 - - - -
1138B ASP* 3.3 11.0 + - + +
1139B ARG* 3.3 36.1 + - - +
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Residues in contact with VAL1136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1186A VAL* 4.1 10.8 - - + -
1187A ASP 3.9 5.6 - - - +
1188A PHE 4.3 4.0 - - - +
1190A GLU* 2.7 46.9 - - + +
1010B VAL* 3.9 31.2 - - + -
1132B ASN* 2.7 32.4 + - - +
1133B ARG 4.1 0.9 - - - +
1135B ALA* 1.3 75.4 - - - +
1137B LEU* 1.3 60.6 + - - +
1139B ARG* 3.3 14.1 + - - +
1140B SER* 3.0 30.5 + - - -
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Residues in contact with LEU1137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1186A VAL* 4.0 3.8 - - + -
1008B GLY 4.3 7.0 - - - +
1010B VAL* 3.5 26.9 - - + -
1016B ALA 3.8 25.8 - - - +
1017B GLY* 4.2 2.2 - - - -
1134B PHE 3.3 10.9 + - - +
1135B ALA 3.2 0.6 - - - -
1136B VAL* 1.3 76.6 - - - +
1138B ASP* 1.3 61.6 + - - +
1141B PHE* 2.6 72.8 + - + +
1144B ASP* 4.4 3.1 - - + -
1145B ALA* 3.6 24.0 - - + +
1148B LEU* 3.8 22.7 - - + -
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Residues in contact with ASP1138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129B MET* 3.9 19.1 - - + +
1134B PHE 3.6 1.4 + - - -
1135B ALA 3.3 10.5 + - - +
1136B VAL 3.2 0.2 - - - -
1137B LEU* 1.3 79.0 - - - +
1139B ARG* 1.3 61.2 + - + +
1142B PRO* 3.3 30.4 - - - +
1145B ALA* 3.4 11.3 - - - +
1146B LYS* 5.2 0.9 - - - +
1149B ARG* 3.0 38.7 + - - +
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Residues in contact with ARG1139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190A GLU 3.1 26.7 + - - -
1191A GLY* 4.1 13.5 + - - -
1077B ARG* 3.1 27.5 - - - +
1132B ASN* 2.7 25.2 - - - +
1135B ALA* 3.3 18.0 + - - +
1136B VAL* 3.3 19.1 + - - +
1137B LEU 3.2 0.4 - - - -
1138B ASP* 1.3 81.1 - - + +
1140B SER* 1.3 64.4 + - - +
1142B PRO* 4.3 5.9 - - - +
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Residues in contact with SER1140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1186A VAL* 3.5 22.9 - - - +
1190A GLU* 5.5 0.5 + - - -
1136B VAL 3.0 16.3 + - - -
1139B ARG* 1.3 81.9 - - - +
1141B PHE* 1.3 93.1 + - - +
1142B PRO* 3.3 8.8 - - - +
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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