Contacts of the helix formed by residues 1034 - 1042 (chain A) in PDB entry 3NC0
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 PHE1034 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A LYS* 4.4 12.6 - - - -
189A VAL* 3.6 26.2 - - + +
190A LYS* 4.0 24.5 - - + -
193A HIS* 4.0 38.8 - + + -
996A LEU* 5.5 0.7 - - - -
1032A ASP 3.2 20.4 - - - -
1033A LEU* 1.3 92.3 - - + +
1035A LEU* 1.3 68.7 + - - +
1037A GLU* 3.6 35.4 - - + +
1038A ARG* 3.0 21.1 + - - +
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Residues in contact with LEU1035 (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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992A ALA* 4.7 23.6 - - + +
996A LEU* 4.1 26.7 - - + -
1033A LEU* 4.0 16.0 - - + -
1034A PHE* 1.3 68.1 - - - +
1036A GLU* 1.3 64.9 + - + +
1037A GLU 2.6 3.8 + - - -
1038A ARG* 2.6 5.0 + - - -
1039A GLU* 2.5 51.0 + - + +
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Residues in contact with GLU1036 (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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1035A LEU* 1.3 77.2 - - + +
1037A GLU* 1.3 64.9 + - - +
1039A GLU* 3.8 15.6 + - - +
1040A THR* 3.2 29.4 + - + +
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Residues in contact with GLU1037 (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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189A VAL* 3.6 29.7 - - + +
192A LYS* 5.5 4.3 - - - +
1034A PHE* 3.6 35.5 - - + +
1035A LEU 2.6 3.6 + - - -
1036A GLU* 1.3 80.6 - - - +
1038A ARG* 1.3 64.2 + - - +
1040A THR* 3.2 4.8 + - - -
1041A ALA* 3.2 18.8 + - + +
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Residues in contact with ARG1038 (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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188A GLN* 3.4 29.7 + - - +
189A VAL* 4.1 26.5 - - + +
996A LEU* 4.3 25.7 - - + +
1004A LEU* 3.8 18.2 - - - +
1010A ALA* 5.1 1.6 + - - +
1014A HIS* 4.0 17.5 + - - +
1017A ASP* 5.8 2.4 + - - -
1034A PHE 3.0 15.9 + - - +
1035A LEU 2.6 5.8 + - - +
1037A GLU* 1.3 77.1 - - - +
1039A GLU* 1.3 63.7 + - - +
1041A ALA* 2.9 24.4 + - - +
1042A LEU* 3.0 44.4 + - + +
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Residues in contact with GLU1039 (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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996A LEU* 5.0 11.8 - - + +
1035A LEU* 2.5 40.5 + - + +
1036A GLU* 3.8 21.5 + - - +
1038A ARG* 1.3 73.2 - - - +
1040A THR* 1.3 64.4 + - + +
1042A LEU* 3.7 14.5 + - - +
1043A ARG* 4.1 10.9 + - - +
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Residues in contact with THR1040 (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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1036A GLU* 3.2 17.8 + - + +
1037A GLU* 3.2 9.5 + - - -
1039A GLU* 1.3 77.8 - - + +
1041A ALA* 1.3 58.4 + - - +
1042A LEU 3.0 4.9 - - - -
1043A ARG* 2.7 31.1 + - - +
1044A GLN* 3.1 9.7 + - - +
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Residues in contact with ALA1041 (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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1004A LEU* 5.8 0.3 - - - +
1037A GLU* 3.2 13.6 + - + +
1038A ARG* 2.9 26.8 + - - +
1040A THR* 1.3 82.6 + - - +
1042A LEU* 1.3 59.7 + - - +
1044A GLN* 3.6 26.3 + - - +
1045A ALA* 3.9 5.9 + - - +
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Residues in contact with LEU1042 (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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996A LEU* 3.7 31.0 - - + +
999A THR* 4.6 7.9 - - + -
1000A GLY* 3.8 22.2 - - - +
1003A SER* 3.7 13.9 - - - +
1004A LEU* 3.9 24.9 - - + -
1014A HIS* 5.1 2.2 - - + +
1038A ARG* 3.0 50.4 + - - +
1039A GLU* 3.8 11.0 - - - +
1040A THR 3.0 0.4 - - - -
1041A ALA* 1.3 78.8 - - - +
1043A ARG* 1.3 63.3 + - + +
1045A ALA* 3.2 8.3 + - - +
1046A GLN* 2.9 23.9 + - - +
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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