Contacts of the helix formed by residues 731 - 740 (chain A) in PDB entry 1N7F
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 PRO 731 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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689A THR 3.8 4.9 - - - +
690A GLU* 3.5 41.3 - - - +
691A GLU 4.9 0.2 - - - +
692A PRO* 4.4 8.7 - - + +
696A ILE* 4.1 3.9 - - - +
729A GLY 4.4 2.9 - - - +
730A LYS* 1.3 95.1 - - + +
732A LEU* 1.3 67.0 + - - +
733A SER* 3.1 17.5 - - - +
734A GLU* 2.9 23.8 + - + +
735A ALA 3.6 2.3 + - - -
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Residues in contact with LEU 732 (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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686A ILE* 3.7 33.4 - - + -
687A SER* 4.3 0.4 - - - -
688A GLY* 3.6 31.6 - - - +
689A THR 2.9 20.2 + - - +
690A GLU* 3.4 5.4 + - - +
696A ILE* 4.0 25.3 - - + +
731A PRO* 1.3 71.6 - - - +
733A SER* 1.3 63.0 + - - +
735A ALA* 3.0 4.5 + - + +
736A ILE* 2.9 37.9 + - + +
4C ARG* 3.7 30.7 - - + +
6C TYR* 5.0 4.7 - - + -
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Residues in contact with SER 733 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A GLU* 2.6 34.1 + - - -
731A PRO* 3.4 11.1 - - - +
732A LEU* 1.3 76.4 - - - +
734A GLU* 1.3 58.0 + - - +
736A ILE* 3.4 14.2 + - - +
737A HIS* 2.9 27.2 + - - +
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Residues in contact with GLU 734 (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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725A SER* 5.1 3.5 - - - -
726A SER 5.1 2.4 - - - +
727A LEU* 4.3 9.6 - - + -
730A LYS* 3.9 35.6 - - + +
731A PRO* 2.9 19.6 + - + +
733A SER* 1.3 78.9 + - - +
735A ALA* 1.3 65.5 + - - +
737A HIS* 3.2 17.2 + - - +
738A LEU* 3.0 39.8 + - + +
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Residues in contact with ALA 735 (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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686A ILE* 4.3 15.9 - - + -
696A ILE* 3.8 24.9 - - + -
722A ILE* 3.9 22.9 - - + +
727A LEU* 4.0 9.6 - - + +
731A PRO 3.6 1.8 + - - -
732A LEU 3.0 10.0 + - - +
734A GLU* 1.3 79.4 - - - +
736A ILE* 1.3 58.6 + - - +
738A LEU* 3.3 4.2 + - - +
739A LEU* 2.9 34.6 + - - +
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Residues in contact with ILE 736 (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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686A ILE* 5.1 0.9 - - + -
732A LEU* 2.9 43.3 + - + +
733A SER* 3.6 12.1 - - - +
735A ALA* 1.3 75.0 - - - +
737A HIS* 1.3 65.9 + - - +
739A LEU* 3.2 8.4 + - - +
740A GLN* 2.9 46.4 + - - +
4C ARG* 6.3 0.2 - - + -
6C TYR* 3.6 52.5 - - + -
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Residues in contact with HIS 737 (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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733A SER 2.9 15.3 + - - +
734A GLU* 3.2 23.3 + - - +
736A ILE* 1.3 76.7 - - - +
738A LEU* 1.3 64.6 + - + +
740A GLN* 3.4 27.8 + - - +
741A MET* 3.5 45.2 + - + +
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Residues in contact with LEU 738 (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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722A ILE* 4.1 26.2 - - + +
723A ASN* 4.6 9.2 - - + +
725A SER* 3.6 38.8 - - - +
727A LEU* 3.9 24.5 - - + -
734A GLU* 3.0 33.2 + - + +
735A ALA* 3.6 5.8 - - - +
737A HIS* 1.3 77.1 - - + +
739A LEU* 1.3 66.1 + - - +
741A MET* 3.0 30.3 + - + +
742A ALA* 3.3 9.9 + - - +
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Residues in contact with LEU 739 (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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682A LEU* 4.5 15.5 - - + -
686A ILE* 3.8 23.1 - - + -
719A ILE* 6.3 0.4 - - + -
722A ILE* 4.0 26.5 - - + -
735A ALA 2.9 21.0 + - - +
736A ILE* 3.2 5.1 + - - +
738A LEU* 1.3 76.4 - - - +
740A GLN* 1.3 63.4 + - - +
741A MET 3.0 0.2 - - - -
742A ALA* 3.1 24.1 + - + +
746A VAL* 4.7 7.9 - - + -
748A LEU* 5.1 2.5 - - + -
6C TYR* 4.2 15.3 - - + -
8C CYS* 3.7 37.7 - - + -
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Residues in contact with GLN 740 (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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736A ILE* 2.9 36.5 + - - +
737A HIS* 3.6 24.5 + - - +
738A LEU 3.2 0.2 - - - -
739A LEU* 1.3 76.9 - - - +
741A MET* 1.3 61.4 + - + +
742A ALA 3.4 1.6 + - - +
6C TYR* 3.8 17.9 + - - +
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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