Contacts of the helix formed by residues 731 - 742 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689B THR 3.8 4.9 - - - +
690B GLU* 3.5 41.1 - - + +
691B GLU 4.8 0.7 - - - +
692B PRO* 4.4 5.6 - - + -
696B ILE* 4.3 2.6 - - - +
727B LEU* 5.2 0.7 - - - +
729B GLY 4.4 2.5 - - - +
730B LYS* 1.3 97.8 - - + +
732B LEU* 1.3 66.1 + - - +
733B SER* 3.3 16.6 - - - +
734B GLU* 2.9 23.6 + - + +
735B ALA* 3.6 3.3 + - - +
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Residues in contact with LEU 732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686B ILE* 3.8 33.9 - - + -
687B SER* 4.1 1.1 - - - -
688B GLY 3.5 18.8 - - - +
689B THR 3.0 17.2 + - - +
690B GLU* 3.4 9.4 + - - +
696B ILE* 3.5 26.9 - - + +
731B PRO* 1.3 71.7 - - - +
733B SER* 1.3 64.2 + - - +
735B ALA* 2.9 14.4 + - - +
736B ILE* 3.0 26.9 + - + +
4D ARG* 3.4 41.7 - - + +
5D THR* 4.3 6.1 - - - +
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Residues in contact with SER 733 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B GLU* 2.7 34.1 + - - -
731B PRO* 3.3 10.7 - - - +
732B LEU* 1.3 77.0 - - - +
734B GLU* 1.3 62.3 + - - +
736B ILE* 3.4 16.6 + - - +
737B HIS* 3.1 21.5 + - - +
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Residues in contact with GLU 734 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726B SER 5.7 0.4 - - - +
727B LEU* 4.5 1.6 - - + -
730B LYS* 3.9 41.4 + - + +
731B PRO* 2.9 18.9 + - + +
733B SER* 1.3 77.6 + - - +
735B ALA* 1.3 61.0 + - - +
737B HIS* 3.1 33.3 + - - +
738B LEU* 2.9 49.7 + - + +
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Residues in contact with ALA 735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686B ILE* 4.1 17.9 - - + -
696B ILE* 4.4 8.7 - - + -
722B ILE* 4.0 17.7 - - + -
727B LEU* 3.9 24.7 - - + +
731B PRO 3.6 2.9 + - - +
732B LEU* 2.9 12.2 + - - +
734B GLU* 1.3 80.0 - - - +
736B ILE* 1.3 62.0 + - - +
738B LEU* 3.3 2.5 + - - +
739B LEU* 3.0 29.9 + - - +
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Residues in contact with ILE 736 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686B ILE* 5.0 0.4 - - + -
732B LEU* 3.0 31.7 + - + +
733B SER* 3.5 17.3 - - - +
734B GLU 3.2 0.2 - - - -
735B ALA* 1.3 76.3 - - - +
737B HIS* 1.3 63.7 + - - +
739B LEU* 3.3 1.9 + - - +
740B GLN* 3.1 50.9 + - - +
5D THR 5.5 1.1 - - - +
6D TYR* 3.8 50.6 - - + -
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Residues in contact with HIS 737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733B SER 3.1 13.8 + - - +
734B GLU* 3.1 33.6 + - - +
736B ILE* 1.3 76.7 - - - +
738B LEU* 1.3 72.0 + - + +
740B GLN* 3.3 13.1 + - - +
741B MET* 3.2 45.5 + - + +
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Residues in contact with LEU 738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722B ILE* 4.0 25.5 - - + +
723B ASN* 5.6 1.4 - - + +
725B SER* 3.8 35.9 - - - +
726B SER 5.3 1.1 - - - +
727B LEU* 3.7 29.8 - - + -
734B GLU* 2.9 36.0 + - + +
735B ALA 3.3 4.2 + - - +
737B HIS* 1.3 83.8 - - + +
739B LEU* 1.3 57.2 + - - +
741B MET* 3.3 5.2 + - + -
742B ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 739 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677B ARG* 2.8 37.9 + - - +
682B LEU* 4.2 14.8 - - + -
686B ILE* 3.8 28.5 - - + -
719B ILE* 6.0 0.9 - - + -
722B ILE* 3.8 27.6 - - + -
735B ALA 3.0 21.3 + - - +
736B ILE 3.7 4.3 - - - +
737B HIS 3.3 0.2 - - - -
738B LEU* 1.3 76.2 - - - +
740B GLN* 1.3 60.1 + - - +
742B ALA* 3.3 4.8 + - - +
746B VAL* 4.1 18.8 - - + -
748B LEU* 4.5 5.8 - - + -
6D TYR* 3.9 15.0 - - + +
8D CYS* 3.7 22.2 - - + -
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Residues in contact with GLN 740 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677B ARG* 4.4 5.5 + - - +
736B ILE* 3.1 32.2 + - - +
737B HIS* 3.3 11.2 + - - +
739B LEU* 1.3 76.2 - - - +
741B MET* 1.3 82.7 + - + +
742B ALA 3.4 0.4 + - - -
743B GLY 4.9 0.3 + - - -
6D TYR* 3.5 25.9 + - - +
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Residues in contact with MET 741 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737B HIS* 3.2 39.9 + - + +
738B LEU* 3.6 4.9 - - + +
739B LEU 3.2 0.4 - - - -
740B GLN* 1.3 114.0 - - + +
742B ALA* 1.3 62.5 + - - +
743B GLY* 3.3 5.1 + - - -
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Residues in contact with ALA 742 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677B ARG* 3.4 13.0 - - - +
722B ILE* 4.9 1.3 - - + -
723B ASN* 3.0 36.1 - - - +
738B LEU 2.9 16.0 + - - +
739B LEU* 3.3 9.0 + - - +
741B MET* 1.3 77.4 - - - +
743B GLY* 1.3 58.8 + - - +
744B GLU 4.1 0.2 + - - -
745B THR 3.3 10.6 + - - +
746B VAL* 3.8 19.5 - - + -
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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