Contacts of the helix formed by residues 1006 - 1013 (chain A) in PDB entry 1FVR
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 ALA1006 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004A TRP 3.7 3.4 + - - -
1005A MET* 1.3 74.6 - - - +
1007A ILE* 1.3 68.4 + - - +
1008A GLU* 3.2 27.1 - - - +
1009A SER* 2.8 17.5 + - - +
1010A LEU* 3.0 11.3 + - - +
1019A SER* 3.8 15.5 + - - +
1022A TRP* 3.6 35.2 - - + -
1023A SER* 5.1 0.4 + - - -
1082A ARG* 3.9 1.3 - - - +
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Residues in contact with ILE1007 (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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1005A MET 3.9 0.4 + - - -
1006A ALA* 1.3 73.6 - - - +
1008A GLU* 1.3 61.7 + - - +
1010A LEU* 3.2 10.6 + - + +
1011A ASN* 2.9 47.1 + - - +
1022A TRP* 3.7 20.6 - - + -
1051A LEU* 3.3 40.2 - - + +
1052A PRO* 3.7 17.5 - - + -
1056A ARG* 3.9 20.9 - - - +
1077A GLU* 4.2 24.5 - - + +
1082A ARG* 5.4 1.1 - - - +
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Residues in contact with GLU1008 (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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1006A ALA* 3.5 9.5 - - + +
1007A ILE* 1.3 78.0 + - - +
1009A SER* 1.3 62.5 + - - +
1011A ASN* 4.5 4.7 - - - +
1012A TYR* 2.8 37.6 + - + +
1014A VAL* 3.7 24.5 - - + +
1016A THR* 4.5 5.7 + - + +
1019A SER* 3.7 13.7 + - - -
1077A GLU 4.6 1.4 - - - +
1079A PRO* 3.6 22.8 - - + +
1082A ARG* 2.8 44.9 + - - -
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Residues in contact with SER1009 (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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1005A MET* 3.7 23.7 - - - +
1006A ALA 2.8 17.1 + - - -
1008A GLU* 1.3 77.4 - - - +
1010A LEU* 1.3 62.0 + - - +
1013A SER* 2.8 27.0 + - - -
1014A VAL 2.8 27.6 + - - +
1015A TYR* 3.7 20.4 - - - -
1019A SER* 3.9 14.9 - - - -
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Residues in contact with LEU1010 (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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1002A VAL* 3.8 21.1 - - + +
1005A MET* 3.8 33.4 - - + +
1006A ALA 3.0 14.3 + - - +
1007A ILE* 3.6 13.5 - - + +
1009A SER* 1.3 77.5 - - - +
1011A ASN* 1.3 67.5 + - - +
1013A SER* 4.7 1.9 + - - -
1047A LEU 4.7 4.9 - - - +
1048A TYR* 3.6 52.8 + - + +
1051A LEU* 3.6 34.5 - - + -
1052A PRO* 5.6 4.3 - - + -
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Residues in contact with ASN1011 (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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1007A ILE* 2.9 37.4 + - - +
1008A GLU* 4.9 0.8 - - - +
1010A LEU* 1.3 83.1 - - - +
1012A TYR* 1.3 95.8 + - + +
1013A SER* 5.3 0.6 + - - -
1048A TYR* 5.5 3.1 - - - +
1052A PRO* 4.7 14.5 - - - +
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Residues in contact with TYR1012 (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 TYR* 3.5 15.8 - - - -
1008A GLU* 2.8 27.6 + - + +
1011A ASN* 1.3 101.2 + - + +
1013A SER* 1.3 72.7 + - - +
1014A VAL* 3.2 17.0 + - + +
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Residues in contact with SER1013 (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 TYR* 3.3 17.3 + - - -
993A VAL 2.9 41.8 + - - -
994A LYS 3.4 13.8 + - - -
1005A MET* 5.7 0.7 - - - -
1009A SER* 2.8 20.5 + - - +
1010A LEU 5.2 1.6 + - - -
1011A ASN 3.8 1.3 + - - -
1012A TYR* 1.3 79.4 - - - +
1014A VAL* 1.3 57.5 + - - +
1015A TYR* 3.7 12.9 - - - -
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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