Contacts of the helix formed by residues 1173 - 1184 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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651A MET* 4.0 26.9 - - + -
653A ARG* 5.8 6.3 - - - +
1171A GLU* 2.8 10.0 + - - +
1172A MET* 1.3 77.0 - - - +
1174A ASP* 1.3 65.8 + - - +
1175A PRO* 3.3 25.5 - - + +
1176A ALA* 3.3 22.7 + - + -
1177A ALA* 3.0 19.6 + - - +
1573A ASP* 3.4 47.1 - - + -
1576A ARG* 3.8 33.7 - - + -
1577A GLN* 3.6 24.0 - - + -
1580A ASN* 5.3 1.1 - - - -
1603A SAH 3.3 28.5 - - - +
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Residues in contact with ASP1174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1172A MET 3.6 3.4 + - - +
1173A TRP* 1.3 74.3 - - - +
1175A PRO* 1.3 74.1 - - + +
1177A ALA* 3.6 5.9 + - - +
1178A GLN* 3.1 38.0 + - - +
1181A ARG* 5.1 1.2 + - - -
1191A THR* 4.3 19.0 + - + +
1568A PHE* 4.9 5.4 - - - -
1566B ARG* 5.2 5.7 + - - -
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Residues in contact with PRO1175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1173A TRP* 3.3 43.3 - - + +
1174A ASP* 1.3 97.2 - - + +
1176A ALA* 1.3 62.8 + - - +
1178A GLN* 3.1 3.8 + - - +
1179A ALA 3.0 19.4 + - - -
1568A PHE* 3.6 24.3 - - + +
1573A ASP* 4.0 15.5 - - + +
1577A GLN* 3.3 22.5 + - - +
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Residues in contact with ALA1176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1150A GLY* 3.7 17.1 - - - +
1151A CYS* 3.7 3.7 - - - +
1171A GLU* 3.5 25.4 - - + -
1173A TRP* 3.3 24.5 + - + +
1175A PRO* 1.3 78.4 - - - +
1177A ALA* 1.3 63.8 + - - +
1179A ALA* 3.2 4.0 + - - +
1180A PHE* 2.9 22.9 + - - +
1577A GLN* 3.5 15.1 - - + +
1603A SAH 4.5 2.2 - - - +
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Residues in contact with ALA1177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1171A GLU* 3.4 26.6 - - + +
1173A TRP 3.0 17.0 + - - +
1174A ASP* 3.8 6.5 - - - +
1176A ALA* 1.3 76.3 - - - +
1178A GLN* 1.3 62.0 + - - +
1180A PHE* 3.4 6.1 + - - +
1181A ARG* 3.1 29.4 + - - +
1189A VAL* 3.8 16.1 - - + +
1191A THR* 3.7 18.4 - - - +
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Residues in contact with GLN1178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1174A ASP* 3.1 29.7 + - - +
1175A PRO 3.1 6.7 + - - +
1177A ALA* 1.3 74.1 - - - +
1179A ALA* 1.3 65.9 + - - +
1181A ARG* 2.7 41.3 + - - +
1182A LEU* 2.9 26.3 + - - +
1568A PHE* 3.6 27.4 - - + -
1181B ARG 4.5 0.3 - - - +
1182B LEU* 3.1 55.0 + - + +
1185B PRO* 6.1 0.2 - - - +
1566B ARG* 4.7 5.9 - - - +
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Residues in contact with ALA1179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1151A CYS* 3.8 13.2 - - + -
1175A PRO 3.0 10.8 + - - +
1176A ALA 3.6 7.4 - - - +
1178A GLN* 1.3 74.8 - - - +
1180A PHE* 1.3 59.9 + - - +
1182A LEU* 3.1 16.0 + - - +
1183A ASN* 2.5 27.7 + - - -
1566A ARG 4.0 12.3 - - - +
1568A PHE* 3.9 14.6 - - - +
1577A GLN* 3.7 23.1 - - - +
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Residues in contact with PHE1180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1146A ASP* 4.1 0.7 - - - -
1149A SER* 3.6 17.7 - - - +
1150A GLY 3.4 19.5 - - - +
1151A CYS 3.6 6.6 + - - -
1152A GLY* 3.5 27.4 - - - -
1155A SER* 3.9 24.9 - - - -
1166A THR* 4.1 7.9 - - + -
1169A ALA* 3.6 17.9 - - + -
1176A ALA 2.9 13.3 + - - +
1177A ALA* 3.5 11.9 - - - +
1178A GLN 3.1 0.2 - - - -
1179A ALA* 1.3 76.2 - - - +
1181A ARG* 1.3 63.7 + - - +
1183A ASN* 2.9 6.5 + - - +
1184A ASN* 2.6 42.3 + - - +
1187A THR* 3.5 23.6 - - + -
1189A VAL* 3.6 18.2 - - + -
1565A TYR* 5.2 0.2 - - - -
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Residues in contact with ARG1181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1174A ASP* 5.1 1.6 + - - -
1177A ALA* 3.1 20.0 + - - +
1178A GLN* 2.7 45.7 + - - +
1180A PHE* 1.3 76.6 - - - +
1182A LEU* 1.3 63.0 + - + +
1183A ASN 3.2 0.9 + - - -
1184A ASN 3.4 22.2 + - - +
1185A PRO* 4.0 1.6 - - - +
1187A THR 5.3 3.8 - - - +
1189A VAL* 2.9 45.4 + - + +
1191A THR* 2.9 28.5 + - - +
1181B ARG* 4.3 37.1 - - + -
1182B LEU* 5.6 1.3 - - + -
1184B ASN 5.6 0.2 - - - -
1185B PRO* 3.7 34.1 + - - +
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Residues in contact with LEU1182 (chain A).
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 2.9 14.2 + - - +
1179A ALA* 3.3 18.4 - - - +
1180A PHE 3.1 0.2 - - - -
1181A ARG* 1.3 79.3 - - + +
1183A ASN* 1.3 62.9 + - - +
1185A PRO* 5.3 2.3 - - - +
1566A ARG* 4.4 12.9 - - + +
1567A PHE 4.0 19.1 - - - +
1568A PHE* 4.1 14.1 - - + -
1178B GLN* 3.4 47.8 + - + +
1181B ARG* 5.6 2.0 - - + -
1182B LEU* 3.9 23.1 - - + -
1568B PHE* 3.6 29.6 - - + -
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Residues in contact with ASN1183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1179A ALA* 2.5 25.5 + - - +
1180A PHE 2.9 2.4 + - - +
1182A LEU* 1.3 79.0 - - - +
1184A ASN* 1.3 73.0 + - - +
1185A PRO* 3.9 7.1 - - - +
1564A SER 4.7 0.3 - - - +
1565A TYR* 3.1 49.0 + - + +
1566A ARG* 3.0 46.6 + - - +
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Residues in contact with ASN1184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1155A SER* 5.1 1.6 - - - -
1156A GLU* 5.4 3.0 + - - +
1159A HIS* 3.4 34.3 + - - +
1166A THR 5.5 0.2 - - - +
1180A PHE* 2.6 47.1 + - - +
1181A ARG* 3.4 10.8 + - - +
1183A ASN* 1.3 93.4 + - - +
1185A PRO* 1.3 65.6 - - - +
1186A GLY 3.1 5.9 + - - +
1187A THR* 3.0 34.0 + - + +
1565A TYR* 4.4 3.8 + - - -
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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