Contacts of the strand formed by residues 1150 - 1160 (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 ALA1150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1048B ILE* 3.8 31.6 - - + -
1094B LEU* 3.8 21.1 - - + +
1095B THR 2.7 18.5 + - - +
1096B PRO* 3.6 0.4 - - + +
1097B CYS* 3.0 21.0 + - - +
1142B PRO* 5.4 0.7 - - + -
1143B LEU 3.9 4.9 - - - +
1144B LEU* 4.0 4.5 - - - +
1148B GLY 4.1 0.6 + - - -
1149B HIS* 1.3 70.1 - - - +
1151B VAL* 1.3 60.2 + - - +
1152B GLY 4.9 2.5 - - - +
1172B VAL* 3.2 15.0 - - + +
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Residues in contact with VAL1151 (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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1097B CYS* 3.7 25.4 - - + -
1101B SER 5.4 1.1 - - - +
1104B LEU* 3.7 38.6 - - + -
1118B ARG* 3.7 31.4 + - - +
1143B LEU* 2.8 14.4 + - + +
1145B CYS* 3.8 17.9 - - + +
1150B ALA* 1.3 73.2 - - - +
1152B GLY* 1.3 58.4 + - - +
1169B PHE* 4.1 7.0 - - + -
1171B PRO* 3.7 6.1 - - - +
1172B VAL* 3.0 27.0 + - + +
1173B GLU* 4.5 1.2 - - - +
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Residues in contact with GLY1152 (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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1048B ILE* 5.1 2.6 - - - +
1142B PRO* 3.4 6.9 - - - +
1143B LEU* 2.9 29.3 + - - +
1150B ALA* 3.7 1.5 - - - +
1151B VAL* 1.3 82.1 + - - +
1153B ILE* 1.3 66.3 + - - +
1154B PHE 4.1 0.2 - - - -
1169B PHE* 3.9 9.0 - - - -
1170B ILE 3.1 13.0 - - - -
1172B VAL* 4.0 9.4 - - - -
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Residues in contact with ILE1153 (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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1046B THR* 3.7 31.2 - - + +
1048B ILE* 3.9 16.2 - - + -
1053B TRP* 4.2 13.7 - - + -
1054B THR* 5.0 8.1 - - - -
1055B VAL* 4.9 3.4 - - + -
1082B LEU* 5.0 1.8 - - + -
1140B GLY* 3.7 28.7 - - - +
1141B GLY 3.5 2.9 - - - +
1152B GLY* 1.3 75.6 - - - +
1154B PHE* 1.3 68.3 + - - +
1155B ARG 3.5 0.3 + - - -
1169B PHE* 3.2 2.7 - - - +
1170B ILE* 2.8 55.2 + - + +
1175B LEU* 4.0 26.0 - - + -
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Residues in contact with PHE1154 (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* 3.9 0.3 - - - +
1106B LEU* 3.5 28.7 - - + -
1135B LEU* 3.9 11.7 - - + -
1138B SER* 3.5 38.1 - - - +
1139B ALA* 3.3 2.0 - - - -
1140B GLY 2.8 28.8 + - - -
1141B GLY 2.8 15.9 + - - +
1143B LEU* 3.8 13.5 - - + +
1153B ILE* 1.3 74.8 - - - +
1155B ARG* 1.3 62.5 + - - +
1156B ALA 3.1 28.3 - - - -
1157B ALA* 3.9 5.8 - - + -
1167B VAL* 3.6 25.8 - - + -
1168B ASP 3.7 5.6 - - - -
1169B PHE* 3.9 1.8 - - - -
7C CYS* 3.5 38.4 - - + -
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Residues in contact with ARG1155 (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* 3.7 20.4 - - + -
1057B HIS* 3.2 22.3 - - - -
1080B LYS 4.4 1.6 - - - -
1081B ASP* 2.8 41.8 + - - +
1139B ALA* 3.7 5.2 - - - +
1154B PHE* 1.3 77.9 - - - +
1156B ALA* 1.3 80.0 + - - +
1168B ASP* 3.0 47.0 + - - +
1169B PHE* 4.3 4.3 - - - -
1170B ILE* 4.3 17.7 - - + -
4C MET* 5.1 4.8 - - - +
6C GLU* 4.1 25.7 + - - +
7C CYS 3.3 8.0 + - - -
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Residues in contact with ALA1156 (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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1154B PHE* 3.1 13.3 - - - -
1155B ARG* 1.3 104.8 - - - +
1157B ALA* 1.3 61.2 + - - +
1168B ASP* 2.8 28.0 + - + -
4C MET* 3.8 18.8 - - + -
5C GLU 3.4 17.5 - - - +
6C GLU* 4.0 4.5 - - + +
7C CYS 4.2 2.2 - - - +
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Residues in contact with ALA1157 (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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1132B ILE* 3.5 22.3 - - + +
1135B LEU* 3.8 24.2 - - + -
1154B PHE* 3.9 7.6 - - + -
1156B ALA* 1.3 76.1 - - - +
1158B VAL* 1.3 60.1 + - - +
1164B ALA* 5.0 1.1 - - + -
1166B ALA 3.2 13.5 - - - +
1167B VAL* 4.2 0.7 - - + -
4C MET* 3.5 6.7 - - - -
5C GLU* 2.6 39.6 + - - +
7C CYS* 4.0 2.6 - - - -
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Residues in contact with VAL1158 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1123B ARG* 6.4 0.2 - - - -
1132B ILE* 4.1 1.3 - - - -
1157B ALA* 1.3 71.4 - - - +
1159B SER* 1.3 59.7 + - - +
1164B ALA* 3.4 4.3 - - - -
1165B LYS* 2.8 39.5 + - + +
1166B ALA* 2.8 34.1 + - + +
2C ASP* 3.4 37.7 - - + +
3C GLU* 3.3 10.3 - - - +
4C MET* 3.6 32.1 - - + +
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Residues in contact with SER1159 (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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1132B ILE* 3.6 15.2 - - - +
1157B ALA 3.9 0.6 + - - -
1158B VAL* 1.3 72.9 - - - +
1160B THR* 1.3 58.2 + - - +
1161B ARG 4.0 0.4 - - - -
1162B GLY* 3.1 33.3 + - - -
1163B VAL 3.4 5.6 - - - -
2C ASP* 3.1 5.4 - - - -
3C GLU* 2.8 37.8 + - - +
5C GLU* 3.7 29.9 + - - -
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Residues in contact with THR1160 (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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1159B SER* 1.3 70.0 - - - +
1161B ARG* 1.3 79.1 + - - +
1163B VAL* 2.9 31.6 + - + +
1165B LYS* 3.2 33.6 - - + +
0C ACE 3.8 7.1 + - + +
1C PHE 2.6 31.7 + - - -
2C ASP* 3.9 2.0 - - - -
3C GLU* 5.2 0.2 - - - -
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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