Contacts of the strand formed by residues 1163 - 1171 (chain B) in PDB entry 3M5M
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 VAL1163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129B PRO* 3.7 26.7 - - + -
1130B ARG 3.6 11.9 - - - +
1131B PRO* 4.4 2.5 - - + -
1159B SER* 3.4 2.3 - - - -
1160B THR* 2.9 44.0 + - + +
1161B ARG* 4.1 6.7 - - + +
1162B GLY* 1.3 79.8 - - - +
1164B ALA* 1.3 70.4 + - - +
1165B LYS* 3.4 2.2 + - + -
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Residues in contact with ALA1164 (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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1126B LEU* 3.6 31.2 - - + +
1129B PRO* 4.3 2.9 - - - +
1130B ARG 2.7 23.0 + - - +
1132B ILE* 3.7 23.5 - - + +
1135B LEU* 4.0 22.9 - - + -
1157B ALA* 5.0 1.6 - - + -
1158B VAL 3.4 8.3 - - - +
1163B VAL* 1.3 79.1 - - - +
1165B LYS* 1.3 60.1 + - - +
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Residues in contact with LYS1165 (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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1125B SER* 3.6 6.1 - - - -
1126B LEU* 3.0 26.8 + - - +
1158B VAL* 2.8 16.6 + - + +
1160B THR* 3.2 44.9 - - + +
1163B VAL* 3.8 5.8 - - + +
1164B ALA* 1.3 75.1 - - - +
1166B ALA* 1.3 66.7 + - + +
0C ACE 4.6 7.6 - - - -
2C ASP* 2.7 29.3 + - + +
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Residues in contact with ALA1166 (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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1123B ARG* 6.0 3.4 - - + -
1124B GLY 3.1 15.0 - - - +
1125B SER* 4.4 4.5 - - - +
1126B LEU* 3.9 4.3 - - - +
1157B ALA* 3.2 8.3 - - - +
1158B VAL* 2.8 43.3 + - + -
1165B LYS* 1.3 85.8 - - + +
1167B VAL* 1.3 67.8 + - - +
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Residues in contact with VAL1167 (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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1106B LEU* 4.4 8.5 - - + -
1116B VAL* 3.8 24.9 - - + -
1123B ARG* 3.3 11.5 - - - -
1124B GLY 2.8 40.5 + - - +
1126B LEU* 3.8 18.6 - - + -
1135B LEU* 4.1 12.1 - - + -
1143B LEU* 4.2 15.5 - - + -
1154B PHE* 3.6 27.8 - - + -
1156B ALA 3.5 4.0 - - - -
1157B ALA* 4.2 0.4 - - + -
1166B ALA* 1.3 80.3 - - - +
1168B ASP* 1.3 59.0 + - - +
1169B PHE* 4.4 4.5 - - + -
4C MET* 5.2 1.6 - - - -
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Residues in contact with ASP1168 (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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1122B SER* 3.3 14.7 + - - +
1123B ARG* 2.7 27.8 + - - +
1154B PHE* 3.7 3.8 - - - -
1155B ARG* 3.0 64.7 + - - +
1156B ALA 2.8 16.6 + - - +
1167B VAL* 1.3 73.9 - - - +
1169B PHE* 1.3 64.6 + - - +
4C MET* 3.8 22.2 - - + -
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Residues in contact with PHE1169 (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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1104B LEU* 4.1 21.5 - - + -
1118B ARG* 3.8 21.5 - - - -
1121B ASP 3.4 25.8 - - - -
1122B SER* 2.9 37.2 + - - -
1123B ARG* 3.5 29.6 - - - -
1124B GLY 4.2 1.3 - - - -
1143B LEU* 3.5 32.5 - - + -
1151B VAL* 4.1 15.5 - - + -
1152B GLY* 3.9 9.6 - - - -
1153B ILE 3.2 15.7 - - - +
1155B ARG* 4.2 1.6 - - - +
1167B VAL* 4.4 4.5 - - + -
1168B ASP* 1.3 82.9 - - - +
1170B ILE* 1.3 71.8 + - - +
1171B PRO* 3.5 2.6 - - + +
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Residues in contact with ILE1170 (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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1055B VAL* 4.6 1.6 - - + -
1080B LYS* 3.5 29.2 - - + +
1081B ASP 3.6 15.9 - - - +
1082B LEU* 4.1 21.1 - - + -
1152B GLY* 3.1 0.9 - - - -
1153B ILE* 2.8 49.7 + - + +
1155B ARG* 4.3 17.5 - - + -
1169B PHE* 1.3 74.6 - - - +
1171B PRO* 1.3 69.9 - - + +
1174B SER* 4.0 16.2 - - - +
1175B LEU* 3.3 30.1 - - + +
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Residues in contact with PRO1171 (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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1118B ARG* 4.5 1.6 - - - +
1121B ASP* 3.4 47.6 - - - +
1122B SER* 4.1 5.6 - - - -
1151B VAL 3.7 9.0 - - - +
1169B PHE* 3.5 12.5 - - + +
1170B ILE* 1.3 86.1 - - + +
1172B VAL* 1.3 66.2 + - - +
1173B GLU* 3.5 18.6 - - + +
1174B SER* 2.9 30.3 + - - +
1175B LEU* 3.3 10.0 + - - +
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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