Contacts of the helix formed by residues 1152 - 1164 (chain B) in PDB entry 5IYB
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 PRO1152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A LEU* 4.0 2.5 - - + -
357A LYS* 3.1 32.1 - - - +
1458A ILE 5.1 1.3 - - - +
1459A MET 3.5 9.4 - - - +
1460A LEU 3.3 20.9 - - - +
1461A GLY* 4.7 2.0 - - - +
1107B LEU 5.0 1.8 - - - +
1108B PHE* 3.6 13.9 - - + -
1112B ASP* 3.4 16.6 - - - +
1114B TYR* 4.5 0.2 - - - -
1151B MET* 1.3 88.6 - - + +
1153B TYR* 1.3 59.3 - - - +
1155B CYS* 2.9 37.0 + - + +
1156B LYS* 2.9 11.1 + - - -
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Residues in contact with TYR1153 (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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81A CYS 5.4 4.2 + - - -
259A SER* 3.8 26.2 + - - -
1069B ILE 4.1 6.9 + - - -
1070B LEU 4.7 0.4 - - - -
1071B ASN* 3.6 17.5 - - - -
1072B ARG* 3.4 55.2 + - + -
1112B ASP* 2.9 23.8 + - - +
1114B TYR* 4.0 24.6 - + + +
1151B MET 3.8 1.6 + - - -
1152B PRO* 1.3 70.8 - - - +
1154B ALA* 1.3 56.0 + - - +
1156B LYS* 3.1 42.2 + - - +
1157B LEU* 2.9 51.5 + - + +
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Residues in contact with ALA1154 (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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349A ARG* 3.6 15.2 - - - +
353A ASN* 3.4 21.5 - - - +
354A LEU* 4.5 8.5 - - - +
357A LYS* 4.2 6.5 - - - +
1071B ASN* 4.3 11.1 + - - +
1073B GLN* 3.3 28.3 - - - +
1112B ASP* 3.0 7.6 + - - +
1153B TYR* 1.3 77.4 - - - +
1155B CYS* 1.3 57.4 + - - +
1157B LEU* 3.5 3.8 + - - +
1158B LEU* 3.1 21.8 + - - +
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Residues in contact with CYS1155 (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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354A LEU* 3.7 16.1 - - + +
1459A MET* 3.4 20.4 - - - +
1460A LEU* 4.1 23.6 - - - -
1151B MET* 4.3 3.6 - - - -
1152B PRO* 2.9 31.0 + - + +
1154B ALA* 1.3 77.9 - - - +
1156B LYS* 1.3 58.3 + - - -
1157B LEU 3.2 0.4 - - - -
1158B LEU* 3.3 6.5 + - - +
1159B PHE* 2.9 42.9 + - - +
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Residues in contact with LYS1156 (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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82A PRO* 3.4 29.1 + - + +
259A SER* 4.6 1.6 + - - -
1114B TYR* 3.4 28.0 - - + -
1116B VAL* 4.1 7.6 - - + -
1125B MET* 4.0 16.2 - - + -
1151B MET* 4.0 17.3 - - - -
1152B PRO 2.9 14.4 + - - +
1153B TYR* 3.1 54.9 + - - +
1155B CYS* 1.3 71.6 - - - +
1157B LEU* 1.3 65.5 + - - +
1159B PHE* 3.3 4.7 + - - +
1160B GLN* 3.0 42.6 + - - +
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Residues in contact with LEU1157 (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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259A SER 3.9 14.6 - - - +
260A VAL* 3.8 33.2 - - + +
349A ARG* 3.7 33.2 - - - +
1070B LEU 3.6 24.0 - - - +
1071B ASN* 4.2 5.4 - - - +
1153B TYR* 2.9 35.6 + - + +
1154B ALA* 3.7 7.2 - - - +
1155B CYS 3.2 0.4 - - - -
1156B LYS* 1.3 75.5 - - - +
1158B LEU* 1.3 67.1 + - - +
1160B GLN* 3.0 9.8 + - - +
1161B GLU* 2.9 30.5 + - - +
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Residues in contact with LEU1158 (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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343A LEU* 3.5 35.7 - - + -
349A ARG* 3.6 23.2 - - + +
350A VAL* 4.1 9.9 - - + -
354A LEU* 3.9 10.1 - - + -
1427A LEU* 5.2 4.7 - - + -
1439A LEU* 5.1 2.2 - - + -
1459A MET* 3.7 29.6 - - + -
1154B ALA 3.1 8.6 + - - +
1155B CYS* 3.3 9.8 + - - +
1157B LEU* 1.3 77.3 - - - +
1159B PHE* 1.3 70.6 + - + +
1161B GLU* 3.6 3.2 + - - +
1162B LEU* 3.1 45.5 + - + +
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Residues in contact with PHE1159 (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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21A VAL* 4.9 15.3 - - + -
23A PHE* 5.9 0.2 - + - -
1427A LEU* 5.3 15.0 - - + -
1460A LEU* 3.9 21.8 - - + -
1125B MET* 4.2 14.1 - - + -
1151B MET* 3.7 34.1 - - + -
1155B CYS* 2.9 27.7 + - - +
1156B LYS 3.5 5.4 - - - +
1158B LEU* 1.3 86.9 - - + +
1160B GLN* 1.3 50.5 + - - +
1162B LEU* 3.5 3.5 - - - +
1163B MET* 2.7 42.8 + - + +
1167B ILE* 3.8 41.1 - - + +
1169B PRO* 4.7 17.7 - - + -
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Residues in contact with GLN1160 (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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82A PRO* 3.1 22.8 + - - +
83A GLY 3.9 9.5 + - - -
85A PHE* 4.2 15.3 - - + -
256A PRO* 5.3 2.1 - - - +
257A PRO* 3.9 11.4 - - - +
259A SER* 4.4 0.7 + - - -
260A VAL* 3.2 33.2 - - + +
1125B MET* 3.7 24.5 + - + +
1156B LYS* 3.0 40.8 + - - +
1157B LEU* 3.0 7.5 + - - +
1159B PHE* 1.3 72.6 - - - +
1161B GLU* 1.3 64.5 + - - +
1163B MET* 3.2 13.1 + - - +
1164B SER* 3.2 19.2 + - - -
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Residues in contact with GLU1161 (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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256A PRO* 6.0 0.2 - - - -
260A VAL* 4.1 21.2 - - + +
339A LEU* 3.6 36.8 - - + +
342A ARG* 5.5 7.3 + - - +
343A LEU* 3.5 30.8 - - + +
349A ARG* 3.2 36.3 + - - +
1157B LEU* 2.9 26.2 + - - +
1158B LEU* 4.1 6.7 - - - +
1160B GLN* 1.3 68.0 - - - +
1162B LEU* 1.3 64.0 + - - +
1164B SER* 2.9 31.0 + - - -
1165B MET 4.0 1.0 + - - -
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Residues in contact with LEU1162 (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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343A LEU* 4.4 14.6 - - + -
1427A LEU* 6.4 0.9 - - + -
1436A VAL* 6.2 2.7 - - + -
1439A LEU* 3.7 37.7 - - + -
1440A MET* 5.6 10.3 - - + -
1158B LEU* 3.1 44.1 + - + +
1159B PHE 3.7 1.6 - - - +
1161B GLU* 1.3 75.0 - - - +
1163B MET* 1.3 59.0 + - - +
1164B SER 3.0 1.8 - - - -
1165B MET* 2.7 14.1 + - + +
1166B SER* 2.7 23.3 + - - -
1167B ILE* 3.4 35.8 - - + +
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Residues in contact with MET1163 (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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26A LEU* 3.1 17.9 - - + +
85A PHE* 3.3 44.3 - - + -
254A PRO* 4.9 1.8 - - - +
1123B GLY 4.3 1.6 - - - +
1124B ILE* 3.9 15.0 - - + -
1125B MET* 3.3 62.6 - - + +
1159B PHE* 2.7 28.1 + - + +
1160B GLN* 3.2 6.6 + - - +
1162B LEU* 1.3 68.6 - - - +
1164B SER* 1.3 58.1 + - - +
1165B MET 2.8 10.8 + - - -
1166B SER* 3.0 14.6 + - - +
1167B ILE* 4.1 22.0 - - + +
1169B PRO* 5.4 2.9 - - + -
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Residues in contact with SER1164 (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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26A LEU* 4.8 1.1 - - - +
85A PHE* 5.2 2.0 - - - -
254A PRO* 3.4 35.4 - - - +
256A PRO* 4.5 18.9 - - - +
339A LEU* 4.4 15.2 - - - +
1160B GLN 3.2 10.3 + - - -
1161B GLU* 2.9 19.5 + - - -
1163B MET* 1.3 75.0 - - - +
1165B MET* 1.3 75.1 + - - +
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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