Contacts of the helix formed by residues 1152 - 1162 (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 GLY1152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1146A ASP* 4.9 0.7 - - - -
1149A SER 3.2 8.3 + - - -
1150A GLY 3.0 5.1 - - - -
1151A CYS* 1.3 81.5 - - - +
1153A GLY* 1.3 67.0 + - - +
1154A LEU 3.3 2.5 - - - -
1155A SER* 4.1 2.8 - - - -
1156A GLU* 2.9 26.0 + - - +
1180A PHE* 3.5 24.2 - - - -
1565A TYR* 3.2 8.3 + - - -
1603A SAH 3.4 0.6 + - - -
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Residues in contact with GLY1153 (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 3.9 1.0 - - - -
1152A GLY* 1.3 74.3 - - - +
1154A LEU* 1.3 63.2 + - - +
1156A GLU* 3.1 5.0 + - - +
1157A GLY* 3.0 19.1 + - - -
1561A PHE* 4.0 16.2 - - - -
1581A ALA* 4.0 9.2 - - - +
1582A VAL 3.3 23.2 - - - +
1584A PRO* 4.0 5.2 - - - +
1603A SAH 3.0 13.2 + - - -
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Residues in contact with LEU1154 (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* 4.4 8.1 - - - +
1152A GLY 3.3 0.4 - - - -
1153A GLY* 1.3 72.9 - - - +
1155A SER* 1.3 64.1 + - - +
1157A GLY 2.9 4.3 + - - -
1158A PHE* 2.9 27.8 + - + +
1224A CYS* 3.7 38.1 - - + -
1225A GLY* 4.2 18.2 - - - +
1267A LEU* 4.0 22.2 - - + -
1269A GLU* 4.9 6.5 - - + -
1582A VAL* 3.8 20.1 + - + -
1587A ALA* 3.4 27.0 - - + +
1590A ILE* 5.7 2.5 - - + -
1603A SAH 2.9 23.1 + - - +
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Residues in contact with SER1155 (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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1144A THR* 5.1 0.5 - - - +
1146A ASP* 3.1 24.9 + - - +
1152A GLY 3.7 3.0 + - - -
1154A LEU* 1.3 78.2 - - - +
1156A GLU* 1.3 53.5 + - - +
1158A PHE* 3.1 10.4 + - - +
1159A HIS* 2.7 47.5 + - - -
1164A SER* 5.4 0.2 + - - -
1166A THR* 3.0 32.1 + - - +
1180A PHE* 3.9 17.8 - - - -
1184A ASN* 5.1 1.3 - - - -
1224A CYS* 4.8 3.9 - - - -
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Residues in contact with GLU1156 (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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1152A GLY 2.9 21.2 + - - +
1153A GLY* 3.2 8.3 - - - +
1154A LEU 3.1 0.2 - - - -
1155A SER* 1.3 76.9 - - - +
1157A GLY* 1.3 58.2 + - - +
1159A HIS* 3.2 15.9 + - - +
1160A GLN* 2.9 60.9 + - - +
1184A ASN* 5.4 1.4 + - - +
1561A PHE* 5.3 0.7 - - + -
1562A PRO* 3.8 11.8 - - + +
1565A TYR* 3.5 32.3 - - + -
1584A PRO* 4.0 13.9 - - + -
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Residues in contact with GLY1157 (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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1153A GLY 3.0 7.3 + - - -
1154A LEU 2.9 7.1 + - - -
1156A GLU* 1.3 74.4 - - - +
1158A PHE* 1.3 65.1 + - - +
1160A GLN* 3.3 8.4 + - - +
1161A ALA 3.1 16.3 + - - -
1584A PRO* 3.5 28.2 - - - +
1587A ALA* 3.6 4.3 - - - -
1588A LYS* 3.3 18.3 - - - -
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Residues in contact with PHE1158 (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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1144A THR* 5.0 1.3 - - + -
1154A LEU* 2.9 22.7 + - + +
1155A SER* 3.5 9.4 - - - +
1157A GLY* 1.3 73.5 - - - +
1159A HIS* 1.3 56.6 + - - +
1161A ALA* 2.8 27.4 + - - +
1162A GLY 2.9 9.4 + - - -
1163A ILE* 3.8 9.7 + - + -
1164A SER* 3.2 24.5 - - - +
1222A MET* 3.4 37.5 - - + -
1224A CYS* 4.0 26.7 - - + -
1267A LEU* 3.6 26.9 - - + -
1587A ALA* 3.3 22.0 - - + -
1590A ILE* 4.5 5.4 - - + -
1591A GLY* 3.8 19.3 - - - -
1594A ILE* 4.3 4.5 - - + -
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Residues in contact with HIS1159 (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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1141A LYS* 5.5 3.1 + - - +
1155A SER* 2.7 28.8 + - - +
1156A GLU* 3.4 15.3 - - - +
1158A PHE* 1.3 71.2 - - - +
1160A GLN* 1.3 56.5 + - + +
1162A GLY* 2.7 25.4 + - - +
1164A SER* 3.2 28.6 + - - -
1165A GLU* 4.3 1.1 - - - -
1166A THR* 2.9 45.7 + - - -
1184A ASN* 3.4 30.2 + - - -
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Residues in contact with GLN1160 (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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1156A GLU* 2.9 46.7 + - - +
1157A GLY* 3.4 8.1 - - - +
1159A HIS* 1.3 77.9 - - + +
1161A ALA* 1.3 61.4 + - - +
1162A GLY* 4.4 0.5 - - - -
1560A GLY 5.0 1.4 + - - -
1562A PRO* 3.7 20.6 - - - +
1584A PRO* 4.2 15.5 - - - +
1585A PRO* 5.0 1.4 - - - +
1588A LYS* 3.7 34.6 + - + +
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Residues in contact with ALA1161 (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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1157A GLY 3.1 6.7 + - - +
1158A PHE 2.8 15.1 + - - +
1160A GLN* 1.3 73.0 - - - +
1162A GLY* 1.3 60.6 + - - +
1163A ILE* 3.5 3.7 - - + +
1588A LYS* 3.8 13.4 - - + +
1591A GLY* 3.7 33.0 - - - +
1592A LEU* 3.7 20.0 - - + +
1595A LYS* 3.0 31.4 + - - +
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Residues in contact with GLY1162 (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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1139A LEU* 5.2 6.6 - - - +
1140A PRO 5.3 0.7 - - - +
1141A LYS* 4.0 25.7 - - - +
1158A PHE 2.9 2.2 + - - -
1159A HIS* 2.7 18.4 + - - -
1160A GLN 4.4 0.9 - - - -
1161A ALA* 1.3 80.5 - - - +
1163A ILE* 1.3 62.5 + - - +
1164A SER 3.6 1.3 - - - -
1595A LYS* 4.2 9.6 - - - -
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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