Contacts of the helix formed by residues 1074 - 1082 (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 SER1074 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1071B LEU* 5.1 0.2 - - - -
1073B GLU* 1.3 80.0 - - - +
1075B ILE* 1.3 60.9 + - - +
1076B GLN* 4.2 4.3 - - - -
1077B ASP* 3.3 31.6 + - - +
1078B TYR* 2.8 29.6 + - - +
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Residues in contact with ILE1075 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1041B ASP* 4.5 7.0 - - - +
1068B GLY* 4.8 4.0 - - - +
1071B LEU* 4.3 19.7 - - + -
1073B GLU 3.7 1.8 + - - -
1074B SER* 1.3 70.5 - - - +
1076B GLN* 1.3 54.6 + - + +
1078B TYR* 3.1 8.2 + - + +
1079B SER* 2.7 47.8 + - - +
1087B TYR* 3.9 47.1 - - + +
1089B LEU* 4.7 19.1 - - + -
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Residues in contact with GLN1076 (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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1074B SER* 3.2 4.5 - - - -
1075B ILE* 1.3 78.3 - - + +
1077B ASP* 1.3 68.1 + - - +
1079B SER* 3.7 8.7 - - - -
1080B GLN* 3.0 44.9 + - + +
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Residues in contact with ASP1077 (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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1073B GLU* 3.7 20.8 - - + +
1074B SER* 3.1 32.8 + - - +
1076B GLN* 1.3 78.8 - - - +
1078B TYR* 1.3 62.9 + - - +
1080B GLN* 3.7 12.6 + - - +
1081B GLY* 3.1 20.3 + - - -
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Residues in contact with TYR1078 (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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1043B ASN* 5.0 0.2 - - - -
1064B THR* 3.3 26.0 + - + +
1066B GLU* 3.6 23.6 - - + +
1071B LEU* 3.8 23.8 - - + -
1073B GLU* 3.9 24.7 + - + -
1074B SER 2.8 17.5 + - - +
1075B ILE* 3.4 8.1 - - + +
1077B ASP* 1.3 74.9 - - - +
1079B SER* 1.3 84.2 + - - +
1081B GLY 3.0 8.8 + - - -
1085B ARG* 3.0 54.1 + - + +
1086B PHE 2.7 32.4 + - - -
1087B TYR* 4.2 13.7 - - + -
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Residues in contact with SER1079 (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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1041B ASP* 5.3 0.9 + - - -
1043B ASN* 2.8 31.6 + - - +
1075B ILE* 2.7 33.4 + - - +
1076B GLN* 3.7 8.8 - - - -
1078B TYR* 1.3 83.2 - - - +
1080B GLN* 1.3 65.5 + - - -
1081B GLY 3.1 0.3 + - - -
1082B GLY 3.4 16.3 - - - +
1085B ARG* 4.1 5.4 - - - +
1398B TRP* 6.0 3.4 - - - -
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Residues in contact with GLN1080 (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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1076B GLN* 3.0 32.1 + - + +
1077B ASP* 4.1 11.5 + - - +
1079B SER* 1.3 81.8 - - - +
1081B GLY* 1.3 63.7 + - - +
1082B GLY* 3.1 3.6 + - - +
1402B GLN* 4.7 17.7 + - - +
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Residues in contact with GLY1081 (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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1077B ASP 3.1 12.2 + - - -
1078B TYR 3.0 5.8 + - - -
1080B GLN* 1.3 78.3 - - - +
1082B GLY* 1.3 55.3 + - - +
1085B ARG* 3.4 22.7 + - - -
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Residues in contact with GLY1082 (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 SER 3.4 9.4 - - - +
1080B GLN 3.1 4.2 + - - +
1081B GLY* 1.3 77.9 - - - +
1083B PRO* 1.3 76.5 - - - +
1084B ASP 3.9 0.3 + - - -
1085B ARG* 3.2 33.3 + - - +
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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