Contacts of the helix formed by residues 687 - 699 (chain J) in PDB entry 1O1F
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 GLU 687 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677J PRO 2.8 11.9 + - - +
678J ASN* 4.1 16.3 - - + +
679J GLU* 3.8 27.6 + - - +
680J THR* 4.7 9.0 + - - +
686J MET* 1.3 72.1 - - - +
688J HIS* 1.3 67.0 + - - +
689J GLU* 4.9 3.4 - - - +
690J LEU* 4.0 22.0 + - + +
691J VAL* 3.0 24.4 + - - +
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Residues in contact with HIS 688 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45J GLN* 4.4 18.8 - - + +
46J SER* 3.8 29.2 + - - +
47J PHE 4.1 8.4 + - - -
48J VAL* 6.0 0.2 - - + -
103J LEU* 4.0 21.6 - - + +
104J TYR* 3.6 25.3 - + - -
107J MLY 2.9 46.5 + - + +
686J MET* 3.8 12.3 - - + -
687J GLU* 1.3 68.7 - - - +
689J GLU* 1.3 63.1 + - - +
690J LEU 2.8 10.9 + - - -
691J VAL* 2.8 15.2 + - - +
692J LEU* 2.8 15.7 + - - +
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Residues in contact with GLU 689 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J SER* 3.5 18.4 - - - +
687J GLU* 4.9 3.6 - - - +
688J HIS* 1.3 78.1 - - - +
690J LEU* 1.3 63.5 + - - +
692J LEU* 3.7 11.6 - - + +
693J HIS* 3.1 40.5 + - + +
696J ARG* 5.7 2.7 - - - +
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Residues in contact with LEU 690 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180J GLU* 5.5 1.3 - - - +
239J ARG* 4.6 11.7 - - - +
676J ILE* 3.0 22.7 - - + +
677J PRO 3.0 32.5 - - - +
678J ASN* 3.9 8.3 - - - -
679J GLU* 3.8 30.7 - - + +
687J GLU* 4.0 23.8 - - + +
688J HIS 2.8 2.8 + - - -
689J GLU* 1.3 82.6 + - - +
691J VAL* 1.3 50.6 + - - +
693J HIS* 3.4 11.1 - - - +
694J GLN* 2.8 37.5 + - - +
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Residues in contact with VAL 691 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103J LEU* 4.5 9.9 - - + -
106J LEU* 4.6 9.9 - - + -
675J ILE* 4.3 17.0 - - + -
676J ILE 4.3 5.2 - - - +
677J PRO* 3.9 13.7 - - + +
686J MET* 3.4 35.9 - - + -
687J GLU 3.0 17.9 - - - +
688J HIS 2.8 7.4 + - - +
690J LEU* 1.3 72.1 - - + +
692J LEU* 1.3 66.9 + - - +
694J GLN* 3.1 9.2 + - - +
695J LEU* 2.9 43.6 + - + +
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Residues in contact with LEU 692 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J SER* 3.6 34.1 - - - +
47J PHE* 4.1 14.4 - - + -
99J GLU* 4.2 28.7 - - + +
103J LEU* 3.6 36.3 - - + -
688J HIS 2.8 9.5 + - - +
689J GLU* 3.7 9.6 - - + +
690J LEU 3.3 0.2 - - - -
691J VAL* 1.3 77.5 - - - +
693J HIS* 1.3 65.4 + - - +
695J LEU* 3.1 21.2 + - + +
696J ARG* 3.0 37.1 + - - +
701J LEU* 4.8 1.1 - - + -
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Residues in contact with HIS 693 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180J GLU* 5.0 8.7 - - - +
469J ILE* 5.1 12.8 - - + +
689J GLU* 3.1 36.8 + - + +
690J LEU* 3.4 13.4 - - - +
692J LEU* 1.3 76.2 - - - +
694J GLN* 1.3 66.7 + - + +
696J ARG* 2.8 34.2 + - - +
697J CYS* 3.2 28.6 + - - -
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Residues in contact with GLN 694 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180J GLU* 4.0 26.9 + - + +
183J ALA* 5.2 0.2 - - - +
674J CYS 4.6 3.0 - - - +
675J ILE* 4.1 14.3 - - + +
676J ILE* 2.7 57.4 + - - +
690J LEU* 2.8 34.8 + - - +
691J VAL* 3.5 10.8 - - - +
693J HIS* 1.3 74.8 - - + +
695J LEU* 1.3 54.7 + - - +
697J CYS* 3.2 5.1 + - - +
698J ASN* 2.6 49.8 + - - +
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Residues in contact with LEU 695 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99J GLU 5.4 0.4 - - - +
102J VAL* 3.8 26.7 - - + -
103J LEU* 4.7 7.0 - - - +
106J LEU* 4.4 13.7 - - + -
675J ILE* 4.7 6.1 - - + -
691J VAL* 2.9 42.7 + - + +
692J LEU* 3.2 26.7 - - + +
693J HIS 3.0 0.4 - - - -
694J GLN* 1.3 81.4 - - + +
696J ARG* 1.3 60.1 + - - +
698J ASN* 3.3 20.6 - - - +
700J VAL* 3.5 15.8 + - + -
701J LEU* 3.0 41.4 + - + -
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Residues in contact with ARG 696 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47J PHE* 5.2 1.2 - - - -
99J GLU* 2.3 43.6 + - - -
584J TYR* 3.8 15.6 - - - -
585J ALA* 4.4 13.2 - - - +
689J GLU* 5.7 2.2 - - - +
692J LEU* 3.0 43.4 + - - +
693J HIS* 2.8 26.9 + - + +
695J LEU* 1.3 71.7 - - - +
697J CYS* 1.3 65.3 - - - +
698J ASN 3.1 5.2 + - - -
699J GLY* 3.9 6.1 + - - -
701J LEU* 4.0 16.5 - - + +
702J GLU* 5.4 4.7 + - - +
705J ARG* 6.0 2.9 - - - +
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Residues in contact with CYS 697 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180J GLU* 5.9 2.5 - - - +
466J GLY* 5.7 1.2 - - - -
467J PHE* 3.7 32.2 + - + +
468J GLU* 5.8 0.2 - - - -
469J ILE* 4.1 21.1 - - - -
484J ASN* 6.0 0.5 - - - -
584J TYR* 3.2 17.3 + - - -
585J ALA* 3.9 28.0 - - + -
693J HIS* 3.2 26.4 + - - +
694J GLN* 3.2 6.0 + - - +
696J ARG* 1.3 80.8 - - - +
698J ASN* 1.3 63.0 + - - +
699J GLY 3.4 0.2 - - - -
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Residues in contact with ASN 698 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122J PHE* 4.7 0.7 - - - -
178J THR* 4.8 12.0 + - - +
179J GLY* 5.4 2.8 - - - -
488J GLN* 3.9 4.3 - - - +
673J ARG* 3.2 54.2 + - + +
674J CYS 4.8 5.5 + - - -
675J ILE* 3.7 21.3 - - - +
694J GLN* 2.6 32.4 + - - +
695J LEU* 3.3 16.0 + - - +
697J CYS* 1.3 78.1 - - - +
699J GLY* 1.3 58.6 + - - +
700J VAL* 3.4 20.6 - - + +
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Residues in contact with GLY 699 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122J PHE* 3.5 14.1 - - - -
488J GLN* 3.5 24.7 - - - -
491J PHE* 4.7 1.9 - - - -
584J TYR* 5.4 1.1 - - - -
695J LEU 3.8 2.2 + - - -
696J ARG 3.9 5.9 + - - -
697J CYS 3.4 1.8 - - - -
698J ASN* 1.3 77.1 - - - +
700J VAL* 1.3 58.0 + - - +
701J LEU 3.3 2.2 - - - -
702J GLU* 2.9 10.0 + - - +
703J GLY* 2.8 26.2 + - - -
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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