Contacts of the helix formed by residues 1187 - 1201 (chain B) in PDB entry 1Q6P
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 SER1187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1185B PRO* 2.9 4.2 + - - +
1186B GLU* 1.3 83.8 - - - +
1188B PRO* 1.3 76.3 - - - +
1189B ALA* 3.0 19.7 + - - +
1190B SER* 3.0 16.2 + - - -
1191B PHE* 3.0 22.9 + - - +
1269B PHE* 3.8 6.9 - - - -
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Residues in contact with PRO1188 (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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1187B SER* 1.3 90.2 - - - +
1189B ALA* 1.3 57.0 + - + +
1191B PHE* 3.7 0.3 - - - +
1192B LEU* 2.9 37.9 + - - +
1269B PHE* 3.8 20.6 - - + -
1272B LEU* 3.1 45.1 - - + -
1273B ALA* 4.6 6.5 - - + -
1276B GLU* 4.1 17.5 - - + +
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Residues in contact with ALA1189 (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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1152B TYR* 5.2 0.2 - - - -
1187B SER* 3.0 9.6 + - - +
1188B PRO* 1.3 78.7 - - - +
1190B SER* 1.3 66.9 + - - +
1192B LEU* 3.9 4.4 - - - +
1193B ASN* 3.0 25.4 + - - +
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Residues in contact with SER1190 (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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1152B TYR* 3.5 42.1 - - - -
1176B TYR* 3.2 21.8 + - - -
1186B GLU* 3.6 7.7 - - - +
1187B SER* 3.0 32.6 + - - -
1189B ALA* 1.3 75.4 - - - +
1191B PHE* 1.3 61.8 + - - +
1193B ASN* 3.5 1.7 - - - +
1194B PHE* 3.0 23.9 + - - +
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Residues in contact with PHE1191 (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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1176B TYR* 4.2 11.6 + + - -
1179B TRP* 3.8 21.3 - + - -
1185B PRO* 3.9 19.5 - - + -
1187B SER 3.0 8.7 + - - +
1188B PRO 3.7 1.8 - - - +
1190B SER* 1.3 77.1 + - - +
1192B LEU* 1.3 72.1 + - + +
1194B PHE* 3.2 7.3 + + - +
1195B LEU* 2.8 36.3 + - + +
1224B THR* 4.5 1.6 - - + -
1225B PHE* 3.8 35.9 - + - -
1228B ALA* 3.5 34.1 - - + -
1269B PHE* 3.5 26.5 - + + -
1273B ALA* 3.9 21.5 - - + -
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Residues in contact with LEU1192 (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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1188B PRO 2.9 22.8 + - - +
1189B ALA* 4.0 4.0 - - - +
1191B PHE* 1.3 89.5 - - + +
1193B ASN* 1.3 58.2 + - - +
1195B LEU* 3.0 7.4 + - + +
1196B PHE* 2.7 55.4 + - + -
1232B LEU* 4.1 17.0 - - + -
1273B ALA* 3.7 16.8 - - + +
1276B GLU* 3.6 16.8 - - + -
1277B GLY* 3.4 36.3 - - - +
1280B PHE* 6.0 1.1 - - + -
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Residues in contact with ASN1193 (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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1152B TYR* 2.8 24.6 + - - +
1153B TYR* 3.6 26.4 + - - -
1189B ALA 3.0 18.0 + - - +
1190B SER 3.5 5.2 - - - +
1192B LEU* 1.3 77.7 - - - +
1194B PHE* 1.3 65.6 + - - +
1196B PHE* 3.2 7.6 + - - +
1197B LYS* 3.0 21.4 + - - +
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Residues in contact with PHE1194 (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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1108B VAL* 3.7 22.2 - - + -
1110B LEU* 3.9 8.3 - - + -
1153B TYR* 3.7 36.8 - + + -
1174B PHE* 3.6 43.3 - + + -
1175B HIS 3.8 4.5 - - - -
1176B TYR* 3.6 40.6 - + + -
1190B SER 3.0 10.5 + - - +
1191B PHE* 3.4 11.4 - + - +
1193B ASN* 1.3 79.8 - - - +
1195B LEU* 1.3 63.6 + - - +
1197B LYS* 3.2 8.9 + - + +
1198B VAL* 3.1 30.2 + - + +
1225B PHE* 3.8 19.7 - + - -
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Residues in contact with LEU1195 (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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1191B PHE* 2.8 25.7 + - + +
1192B LEU* 3.4 16.8 - - + +
1194B PHE* 1.3 82.6 - - - +
1196B PHE* 1.3 60.1 + - + +
1198B VAL* 3.3 3.3 + - + +
1199B ARG* 3.0 36.7 + - + +
1204B LEU* 4.9 3.1 - - + -
1225B PHE* 3.8 31.0 - - + +
1229B ASP* 3.8 37.2 - - + +
1232B LEU* 3.8 29.2 - - + -
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Residues in contact with PHE1196 (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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1192B LEU* 2.7 56.1 + - + +
1193B ASN* 3.8 6.1 - - - +
1195B LEU* 1.3 75.2 - - + +
1197B LYS* 1.3 61.7 + - - +
1199B ARG* 3.2 38.6 + - + +
1200B GLU* 2.8 41.9 + - - +
1232B LEU* 5.0 1.3 - - + -
1277B GLY* 4.6 6.3 - - - -
1280B PHE* 4.3 24.9 - + - -
1281B ILE* 4.0 27.4 - - + -
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Residues in contact with LYS1197 (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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1150B LYS* 5.3 2.9 - - - +
1153B TYR* 3.8 28.3 - - + +
1155B VAL* 4.6 11.2 - - + -
1174B PHE* 4.1 16.0 - - + -
1193B ASN 3.0 12.7 + - - +
1194B PHE* 3.5 11.0 - - + +
1196B PHE* 1.3 75.9 - - - +
1198B VAL* 1.3 65.3 + - - +
1200B GLU* 3.5 25.8 + - - +
1201B SER* 3.1 34.1 + - - +
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Residues in contact with VAL1198 (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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1108B VAL* 4.2 17.7 - - + -
1174B PHE* 3.9 37.0 - - + -
1194B PHE* 3.1 35.4 + - + +
1195B LEU* 3.5 7.6 - - - +
1197B LYS* 1.3 76.2 - - - +
1199B ARG* 1.3 61.5 + - - +
1201B SER* 2.7 23.4 + - - -
1202B GLY 3.9 0.7 + - - -
1203B SER* 4.0 7.1 + - - -
1204B LEU* 3.9 30.1 - - + +
1211B VAL* 5.3 0.4 - - + -
1225B PHE* 4.4 9.0 - - + -
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Residues in contact with ARG1199 (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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1079B ARG* 3.7 7.8 - - - +
1195B LEU* 3.0 22.1 + - + +
1196B PHE* 3.4 32.7 - - + +
1197B LYS 3.2 0.2 - - - -
1198B VAL* 1.3 78.3 - - - +
1200B GLU* 1.3 61.9 + - - +
1202B GLY* 3.2 15.2 + - - -
1204B LEU* 3.8 25.9 + - + +
1229B ASP* 2.8 41.8 + - - +
1232B LEU* 3.4 19.1 - - - +
1233B LEU* 3.9 15.2 - - - +
1281B ILE* 3.8 24.5 - - - +
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Residues in contact with GLU1200 (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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1196B PHE* 2.8 40.3 + - - +
1197B LYS* 3.4 33.6 + - - +
1199B ARG* 1.3 69.8 - - - +
1201B SER* 1.3 63.1 + - - +
1202B GLY* 3.1 3.1 + - - -
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Residues in contact with SER1201 (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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1105B ARG* 3.9 14.4 + - - -
1172B LEU* 3.7 11.8 - - - +
1174B PHE* 3.3 22.9 - - - -
1197B LYS* 3.1 21.7 + - - +
1198B VAL 2.7 16.9 + - - -
1200B GLU* 1.3 77.9 - - - +
1202B GLY* 1.3 58.7 + - - +
1203B SER* 2.6 24.6 + - - -
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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