Contacts of the helix formed by residues 1173 - 1184 (chain B) in PDB entry 3PT6
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 TRP1173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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651B MET* 4.1 27.8 - - + -
699B VAL* 4.5 14.6 - - + +
1171B GLU* 3.1 18.8 + - - +
1172B MET* 1.3 75.8 - - - +
1174B ASP* 1.3 67.8 + - - +
1175B PRO* 3.6 21.4 - - + +
1176B ALA* 3.1 22.9 + - + +
1177B ALA* 3.0 18.7 + - - +
1573B ASP* 3.6 45.3 - - + -
1576B ARG* 3.6 40.4 - - + -
1577B GLN* 3.8 20.6 - - + -
1580B ASN* 5.3 0.9 - - - -
1603B SAH 3.4 17.0 + - - +
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Residues in contact with ASP1174 (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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1566A ARG* 5.0 6.1 + - - -
1172B MET 3.4 4.9 + - - -
1173B TRP* 1.3 72.1 - - - +
1175B PRO* 1.3 68.7 - - + +
1177B ALA* 3.2 6.8 + - - +
1178B GLN* 2.8 56.3 + - - +
1181B ARG* 4.7 4.7 + - - -
1191B THR* 4.2 17.1 + - - +
1568B PHE* 5.0 3.6 - - - -
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Residues in contact with PRO1175 (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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1173B TRP* 3.4 31.0 - - + +
1174B ASP* 1.3 94.5 - - + +
1176B ALA* 1.3 65.5 + - - +
1178B GLN* 3.3 3.5 + - - +
1179B ALA* 3.1 18.2 + - - +
1568B PHE* 3.8 21.7 - - + +
1569B GLY* 5.2 0.2 - - - -
1573B ASP* 3.5 27.1 - - - +
1577B GLN* 3.5 22.2 + - - +
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Residues in contact with ALA1176 (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 GLY* 3.8 21.1 - - - +
1151B CYS* 3.9 2.4 - - - +
1171B GLU* 3.6 19.5 - - + -
1173B TRP* 3.1 30.8 + - + +
1175B PRO* 1.3 77.5 - - - +
1177B ALA* 1.3 65.9 + - - +
1179B ALA* 3.1 5.7 + - - +
1180B PHE 3.0 19.4 + - - -
1577B GLN* 3.9 14.6 - - + +
1603B SAH 4.7 0.9 - - - +
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Residues in contact with ALA1177 (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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1171B GLU* 3.6 26.8 - - + +
1173B TRP 3.0 12.7 + - - +
1174B ASP 3.5 8.5 - - - +
1176B ALA* 1.3 76.5 - - - +
1178B GLN* 1.3 62.8 + - - +
1180B PHE* 3.3 6.6 + - - +
1181B ARG* 3.1 39.2 + - - +
1189B VAL* 3.9 16.2 - - + +
1191B THR* 4.2 9.2 - - - +
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Residues in contact with GLN1178 (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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1182A LEU* 3.4 44.1 + - + +
1566A ARG* 5.1 7.1 - - - +
1174B ASP* 2.8 37.0 + - - +
1175B PRO 3.5 7.0 - - - +
1176B ALA 3.1 0.2 - - - -
1177B ALA* 1.3 75.4 - - - +
1179B ALA* 1.3 55.0 + - - +
1181B ARG* 2.7 59.3 + - - +
1182B LEU* 2.8 15.7 + - - +
1568B PHE* 3.6 34.2 - - + -
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Residues in contact with ALA1179 (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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1151B CYS* 3.7 15.0 - - + -
1175B PRO 3.1 6.4 + - - +
1176B ALA 3.1 8.3 + - - +
1178B GLN* 1.3 78.2 - - - +
1180B PHE* 1.3 63.5 + - - +
1182B LEU* 3.0 14.1 + - - +
1183B ASN* 2.7 24.8 + - - -
1566B ARG 3.8 13.2 - - - +
1568B PHE* 3.9 12.6 - - - +
1577B GLN* 3.7 23.3 - - - +
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Residues in contact with PHE1180 (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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1146B ASP* 4.9 0.2 - - + -
1149B SER* 3.6 22.4 - - - +
1150B GLY 3.5 24.0 - - - +
1151B CYS 3.8 7.7 + - - -
1152B GLY* 3.5 24.9 - - - -
1155B SER* 3.8 24.0 - - - -
1166B THR* 4.1 9.0 - - + -
1169B ALA* 4.0 15.0 - - + -
1176B ALA 3.0 7.6 + - - +
1177B ALA* 3.5 11.7 - - - +
1179B ALA* 1.3 75.8 - - - +
1181B ARG* 1.3 63.4 + - - +
1183B ASN* 3.0 2.8 + - - +
1184B ASN* 3.0 40.7 + - - +
1187B THR* 3.4 22.9 - - + -
1189B VAL* 3.7 18.2 - - + -
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Residues in contact with ARG1181 (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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1178A GLN* 4.5 0.3 - - - +
1181A ARG* 4.3 38.9 - - + -
1182A LEU* 5.6 1.8 - - + -
1185A PRO* 3.6 28.9 + - - +
1174B ASP* 4.7 3.6 + - - -
1177B ALA* 3.1 29.4 + - - +
1178B GLN* 2.7 45.7 + - - +
1180B PHE* 1.3 72.7 - - - +
1182B LEU* 1.3 60.5 + - + +
1183B ASN 3.1 1.2 + - - -
1184B ASN 3.3 23.4 + - - +
1185B PRO 4.1 1.0 - - - -
1187B THR 5.4 1.3 - - - +
1189B VAL* 2.9 49.1 + - + +
1191B THR* 3.5 27.1 - - - +
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Residues in contact with LEU1182 (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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1178A GLN* 3.1 60.1 + - + +
1181A ARG* 5.6 1.8 - - + -
1182A LEU* 3.9 20.2 - - + -
1568A PHE* 3.8 19.3 - - + -
1178B GLN 2.8 11.5 + - - +
1179B ALA* 3.0 11.8 + - - +
1181B ARG* 1.3 77.9 - - - +
1183B ASN* 1.3 62.3 + - - +
1185B PRO* 6.1 0.8 - - - +
1566B ARG* 4.1 17.8 - - + +
1567B PHE 4.4 7.0 - - - +
1568B PHE* 3.8 38.1 - - + -
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Residues in contact with ASN1183 (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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1156B GLU* 5.7 0.9 - - - +
1179B ALA 2.7 23.7 + - - +
1180B PHE 3.0 2.0 + - - +
1182B LEU* 1.3 79.5 - - - +
1184B ASN* 1.3 76.2 + - - +
1185B PRO* 3.9 7.5 - - - +
1564B SER 5.0 0.2 - - - -
1565B TYR* 3.0 48.5 - - + +
1566B ARG* 2.8 48.3 + - - +
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Residues in contact with ASN1184 (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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1181A ARG* 5.6 0.2 - - - -
1155B SER* 5.5 1.1 - - - -
1156B GLU* 5.7 1.2 + - - -
1159B HIS* 3.3 33.9 + - - -
1166B THR* 5.4 1.2 + - - -
1180B PHE* 3.0 39.6 + - + +
1181B ARG* 3.3 13.1 + - - +
1182B LEU 3.6 0.2 - - - -
1183B ASN* 1.3 94.3 + - - +
1185B PRO* 1.3 67.7 - - - +
1186B GLY 3.2 4.0 - - - +
1187B THR* 3.0 36.8 + - + +
1565B TYR* 4.1 6.4 + - - -
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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