Contacts of the helix formed by residues 1063 - 1069 (chain A) in PDB entry 2CFV
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 ALA1063 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1061A GLU 3.7 1.8 + - - -
1062A LEU* 1.3 73.4 - - - +
1064A GLU* 1.3 70.5 + - + +
1065A ASN 3.2 1.0 + - - -
1066A ARG* 3.3 19.1 + - - +
1067A GLY 5.1 0.2 + - - -
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Residues in contact with GLU1064 (chain A).
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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1062A LEU* 3.8 15.2 - - - +
1063A ALA* 1.3 86.8 + - + +
1065A ASN* 1.3 60.2 + - - +
1066A ARG 3.5 0.8 + - - -
1067A GLY* 4.7 3.0 + - - -
1068A LYS* 3.8 15.2 - - - +
1089A HIS* 5.0 9.9 - - - -
1091A THR* 3.9 35.3 - - + +
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Residues in contact with ASN1065 (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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1059A ALA* 3.0 31.3 + - - +
1060A ALA 4.3 3.4 - - - +
1062A LEU* 3.2 16.0 + - - +
1064A GLU* 1.3 75.8 - - - +
1066A ARG* 1.3 63.7 + - - +
1067A GLY 3.5 1.8 - - - -
1068A LYS* 2.9 48.1 + - - +
1069A ASN* 3.2 15.5 + - - -
1091A THR* 3.1 21.9 + - - +
1093A ASP* 5.4 0.6 + - - -
1094A TYR* 3.2 35.6 - - + +
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Residues in contact with ARG1066 (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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1060A ALA 5.2 1.1 - - - -
1062A LEU 3.6 5.4 + - - +
1063A ALA* 3.3 17.4 + - - +
1064A GLU 3.5 0.2 - - - -
1065A ASN* 1.3 76.0 - - - +
1067A GLY* 1.3 57.3 + - - +
1068A LYS 3.1 4.9 + - - -
1069A ASN* 3.3 26.8 + - - +
1072A ASN* 5.0 4.5 - - - +
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Residues in contact with GLY1067 (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 ALA 5.1 0.2 + - - -
1064A GLU 4.7 3.2 + - - -
1065A ASN* 3.5 0.8 - - - +
1066A ARG* 1.3 77.2 - - - +
1068A LYS* 1.3 55.8 + - - +
1069A ASN 3.4 1.6 - - - -
1116A LEU* 3.3 14.2 - - - +
1118A ASN* 2.8 30.6 + - - +
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Residues in contact with LYS1068 (chain A).
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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1064A GLU 3.8 13.2 - - - +
1065A ASN* 2.9 31.8 + - - +
1066A ARG 3.1 1.6 - - - -
1067A GLY* 1.3 81.3 - - - +
1069A ASN* 1.3 60.8 + - - +
1091A THR* 2.7 41.6 + - - +
1092A ASP* 4.3 4.6 - - - +
1094A TYR* 3.8 27.7 + - + +
1095A ILE* 5.8 1.1 - - - -
1096A ASN* 4.1 6.2 + - - +
1113A GLN* 3.0 22.0 + - - -
1116A LEU* 3.7 4.1 - - - +
1118A ASN* 4.6 4.5 - - - +
1119A THR* 3.7 19.9 - - + +
1122A ASP* 4.4 10.1 + - - +
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Residues in contact with ASN1069 (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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1060A ALA 3.3 22.0 + - - -
1065A ASN 3.2 20.3 + - - -
1066A ARG* 3.3 17.0 + - - +
1067A GLY* 3.4 0.9 - - - -
1068A LYS* 1.3 78.9 - - - +
1070A ARG* 1.3 64.9 + - - +
1071A TYR 3.6 18.3 + - - +
1072A ASN* 4.5 6.8 - - - +
1075A LEU* 3.3 16.2 - - + +
1094A TYR* 2.4 28.5 + - - -
1096A ASN* 2.7 16.6 + - - +
1113A GLN* 3.8 3.6 - - - -
1116A LEU* 3.9 5.6 - - - +
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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