Contacts of the helix formed by residues 687 - 699 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677A PRO 2.8 11.4 + - - +
678A ASN* 4.1 17.6 - - + +
679A GLU* 3.8 26.5 + - - +
680A THR* 4.7 8.7 + - - +
686A MET* 1.3 73.5 - - - +
688A HIS* 1.3 65.1 + - - +
689A GLU* 4.9 3.2 - - - +
690A LEU* 4.0 21.9 + - + +
691A VAL* 3.0 23.7 + - - +
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Residues in contact with HIS 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLN* 4.4 18.4 - - + +
46A SER* 3.8 29.3 + - - +
47A PHE 4.1 8.6 + - - -
48A VAL* 6.0 0.4 - - + -
103A LEU* 4.0 21.6 - - + +
104A TYR* 3.6 26.4 - + - -
107A MLY 2.9 46.9 + - + +
686A MET* 3.8 13.2 - - + -
687A GLU* 1.3 69.1 - - - +
689A GLU* 1.3 63.0 + - - +
690A LEU 2.8 11.1 + - - -
691A VAL* 2.8 6.4 + - - +
692A LEU* 2.8 23.7 + - - +
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Residues in contact with GLU 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER* 3.5 17.9 - - - +
687A GLU* 4.9 3.7 - - - +
688A HIS* 1.3 79.0 - - - +
690A LEU* 1.3 64.7 + - - +
692A LEU* 3.7 11.3 - - + +
693A HIS* 3.1 40.9 + - + +
696A ARG* 5.7 2.7 - - - +
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Residues in contact with LEU 690 (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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180A GLU* 5.5 1.6 - - - +
239A ARG* 4.6 11.4 - - - +
676A ILE* 3.0 23.1 - - + +
677A PRO 3.0 32.3 - - - +
678A ASN* 3.9 8.1 - - - -
679A GLU* 3.8 30.7 - - + +
687A GLU* 4.0 23.4 + - + +
688A HIS 2.8 1.8 + - - -
689A GLU* 1.3 84.8 + - - +
691A VAL* 1.3 51.9 + - - +
693A HIS* 3.4 11.0 - - - +
694A GLN* 2.8 38.4 + - - +
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Residues in contact with VAL 691 (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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103A LEU* 4.5 9.6 - - + -
106A LEU* 4.6 9.2 - - + -
675A ILE* 4.3 17.0 - - + -
676A ILE 4.3 7.4 - - - +
677A PRO* 3.9 13.2 - - + +
686A MET* 3.4 35.4 - - + -
687A GLU 3.0 18.2 - - - +
688A HIS 2.8 7.6 + - - +
690A LEU* 1.3 69.7 - - - +
692A LEU* 1.3 67.7 + - - +
694A GLN* 3.1 8.1 + - - +
695A LEU* 2.9 43.4 + - + +
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Residues in contact with LEU 692 (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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46A SER* 3.6 34.3 - - - +
47A PHE* 4.1 15.0 - - + -
99A GLU* 4.2 28.9 - - + +
103A LEU* 3.7 36.3 - - + +
688A HIS 2.8 9.2 + - - +
689A GLU* 3.7 9.6 - - + +
690A LEU 3.3 0.2 - - - -
691A VAL* 1.3 77.7 - - - +
693A HIS* 1.3 65.1 + - - +
695A LEU* 3.1 20.5 + - + +
696A ARG* 3.0 36.3 + - - +
701A LEU* 4.8 0.9 - - + -
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Residues in contact with HIS 693 (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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180A GLU* 5.0 8.7 - - - +
469A ILE* 5.1 12.1 - - + +
689A GLU* 3.1 38.6 + - + +
690A LEU* 3.4 13.0 - - - +
692A LEU* 1.3 76.8 - - - +
694A GLN* 1.3 66.2 + - + +
696A ARG* 2.8 35.4 + - + +
697A CYS* 3.2 28.6 + - - -
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Residues in contact with GLN 694 (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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180A GLU* 4.0 27.2 + - + +
674A CYS 4.6 2.6 - - - +
675A ILE* 4.1 14.2 - - + +
676A ILE* 2.7 59.4 + - - +
690A LEU* 2.8 33.8 + - - +
691A VAL* 3.4 11.4 - - - +
693A HIS* 1.3 75.3 - - + +
695A LEU* 1.3 55.0 + - - +
696A ARG 3.0 0.2 + - - -
697A CYS* 3.2 5.9 + - - +
698A ASN* 2.6 49.3 + - - +
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Residues in contact with LEU 695 (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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99A GLU 5.4 0.4 - - - +
102A VAL* 3.8 26.7 - - + -
103A LEU* 4.7 7.2 - - + +
106A LEU* 4.4 14.8 - - + -
675A ILE* 4.7 6.1 - - + -
691A VAL* 2.9 43.3 + - + +
692A LEU* 3.2 26.9 - - + +
694A GLN* 1.3 80.5 - - + +
696A ARG* 1.3 59.2 + - - +
698A ASN* 3.3 21.2 - - - +
700A VAL* 3.5 15.7 + - + -
701A LEU* 3.0 40.7 + - + -
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Residues in contact with ARG 696 (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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47A PHE* 5.2 1.2 - - - -
99A GLU* 2.3 43.2 + - - +
584A TYR* 3.8 14.9 - - - -
585A ALA* 4.4 13.4 - - - +
689A GLU* 5.7 2.8 - - - +
692A LEU* 3.0 43.9 + - - +
693A HIS* 2.8 25.7 + - - +
695A LEU* 1.3 71.3 - - - +
697A CYS* 1.3 66.5 + - - +
698A ASN 3.1 5.2 + - - -
699A GLY* 3.9 6.4 + - - -
701A LEU* 4.0 17.2 - - + +
702A GLU* 5.4 5.2 + - - +
705A ARG* 6.0 3.1 - - - +
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Residues in contact with CYS 697 (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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178A THR* 5.8 1.6 - - - +
180A GLU* 5.9 2.7 - - - +
466A GLY* 5.7 1.2 - - - -
467A PHE* 3.7 32.3 + - + +
468A GLU* 5.8 0.7 - - - -
469A ILE* 4.1 20.9 - - - -
484A ASN* 6.0 0.3 - - - -
584A TYR* 3.2 18.4 + - - -
585A ALA* 3.9 27.1 - - + -
693A HIS* 3.2 26.2 + - - +
694A GLN* 3.2 5.8 + - - +
696A ARG* 1.3 81.2 - - - +
698A ASN* 1.3 63.0 + - - +
699A GLY 3.4 0.2 - - - -
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Residues in contact with ASN 698 (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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122A PHE* 4.7 0.9 - - - -
178A THR* 4.8 10.6 + - - +
179A GLY* 5.4 3.0 - - - -
488A GLN* 3.9 4.2 - - - +
673A ARG* 3.2 54.4 + - + +
674A CYS 4.8 5.9 + - - -
675A ILE* 3.7 21.9 - - - +
694A GLN* 2.6 31.3 + - - +
695A LEU* 3.3 15.9 + - - +
697A CYS* 1.3 79.1 - - - +
699A GLY* 1.3 57.7 + - - +
700A VAL* 3.4 20.5 + - + +
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Residues in contact with GLY 699 (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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122A PHE* 3.5 14.5 - - - -
488A GLN* 3.5 24.0 - - - -
491A PHE* 4.7 1.7 - - - -
584A TYR* 5.2 2.2 - - - -
695A LEU 3.8 1.8 + - - -
696A ARG 3.9 5.5 + - - -
697A CYS 3.4 1.6 - - - -
698A ASN* 1.3 77.6 - - - +
700A VAL* 1.3 57.3 + - - +
701A LEU 3.2 2.9 - - - -
702A GLU* 2.9 9.5 + - - +
703A GLY* 2.8 26.5 + - - -
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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