Contacts of the helix formed by residues 1065 - 1072 (chain A) in PDB entry 4C3I
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 GLN1065 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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791A TYR* 3.5 39.0 + - + +
1061A SER 3.4 13.5 - - - +
1062A HIS* 3.0 26.9 + - + +
1064A THR* 1.3 79.4 + - - +
1066A PHE* 1.3 58.4 + - - +
1067A GLU 3.5 2.7 - - - -
1068A PHE* 3.4 19.4 + - + +
1069A CYS* 3.0 30.0 + - - -
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Residues in contact with PHE1066 (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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1063A MET 3.6 22.4 - - - -
1064A THR* 2.9 31.8 + - + -
1065A GLN* 1.3 68.4 - - - +
1067A GLU* 1.4 61.3 + - - +
1069A CYS* 3.3 2.3 + - - -
1070A LEU* 2.8 26.3 + - - +
1140A PHE* 4.4 7.2 - + - -
1143A LYS* 3.6 28.0 - - + -
1144A LEU* 3.6 41.1 - - + -
1147A PHE* 3.6 42.6 - + + -
1166A PHE* 3.4 12.4 - + + -
1170A MET* 3.7 24.9 - - + -
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Residues in contact with GLU1067 (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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1065A GLN 3.5 0.6 - - - -
1066A PHE* 1.4 75.0 - - - +
1068A PHE* 1.4 57.3 + - - +
1070A LEU* 3.2 5.6 + - - +
1071A ASP* 2.9 41.5 + - - +
1147A PHE* 3.8 17.3 - - + -
1151A ASN* 4.6 6.1 + - - -
1153A LYS* 3.3 30.0 + - - +
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Residues in contact with PHE1068 (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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747A ILE* 4.4 1.8 - - + -
748A ASN 3.8 10.8 - - - -
749A LEU* 4.3 16.2 - - + -
796A SER* 3.6 45.8 - - - -
799A GLU* 4.4 8.5 - - + -
800A VAL* 3.7 16.6 - - + -
1062A HIS* 3.5 30.1 - + + -
1065A GLN* 3.4 24.4 + - + +
1066A PHE 3.3 0.4 - - - -
1067A GLU* 1.4 76.6 - - - +
1069A CYS* 1.4 68.0 + - - +
1071A ASP* 3.2 9.3 + - - +
1072A ASN* 3.1 53.4 + - + -
1076A LEU* 5.0 2.2 - - + -
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Residues in contact with CYS1069 (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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1062A HIS* 3.4 19.3 - - - -
1065A GLN 3.0 21.2 + - - +
1066A PHE 3.6 4.5 - - - +
1068A PHE* 1.4 80.6 - - - +
1070A LEU* 1.4 56.3 + - - +
1072A ASN 3.1 3.6 - - - +
1073A TYR* 3.0 27.0 + - - +
1076A LEU* 3.7 22.5 - - + +
1166A PHE* 4.0 4.7 - - + -
1169A LEU* 4.3 5.5 - - + +
1170A MET* 3.7 32.1 - - - -
1173A LYS* 4.0 15.5 - - - -
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Residues in contact with LEU1070 (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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1066A PHE 2.8 17.2 + - - +
1067A GLU* 3.2 7.4 + - - +
1069A CYS* 1.4 75.3 - - - +
1071A ASP* 1.4 64.8 + - - +
1072A ASN 3.1 1.3 - - - -
1073A TYR* 3.2 19.3 + - + +
1147A PHE* 4.4 16.4 - - + -
1153A LYS* 3.9 35.7 - - + +
1161A VAL* 4.0 29.4 - - + +
1166A PHE* 3.6 27.5 - - + -
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Residues in contact with ASP1071 (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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748A ASN* 3.5 43.2 + - + +
749A LEU* 5.6 0.3 - - - -
750A ILE* 4.7 17.4 + - - +
1067A GLU* 2.9 26.7 + - - +
1068A PHE* 3.6 9.1 - - - +
1070A LEU* 1.4 78.7 - - - +
1072A ASN* 1.3 58.1 + - - +
1073A TYR 3.6 0.8 + - - -
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Residues in contact with ASN1072 (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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746A GLY 4.0 2.1 - - - +
747A ILE* 3.8 6.5 - - - +
748A ASN* 2.8 53.9 + - - +
800A VAL* 4.0 20.8 - - + +
1068A PHE* 3.1 40.5 + - - +
1069A CYS 3.1 4.7 - - - +
1070A LEU 3.1 0.2 - - - -
1071A ASP* 1.3 75.7 - - - +
1073A TYR* 1.4 62.5 - - - +
1074A TYR 3.6 1.8 - - - -
1075A ALA* 3.4 11.4 + - + +
1076A LEU* 3.0 29.3 + - + +
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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