Contacts of the helix formed by residues 692 - 705 (chain O) in PDB entry 5MQF
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 THR 692 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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690O GLU 3.7 0.8 - - - -
691O GLU* 1.3 73.4 - - - +
693O GLU* 1.3 63.0 - - - +
694O ARG* 2.2 23.9 + - - +
695O THR 2.5 15.2 + - - -
696O ARG* 3.3 9.9 - - - +
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Residues in contact with GLU 693 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692O THR* 1.3 74.6 - - - +
694O ARG* 1.3 50.1 + - - +
696O ARG* 3.0 20.7 - - - +
697O ASN* 2.6 34.9 + - - +
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Residues in contact with ARG 694 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686O GLU* 6.4 0.2 - - - -
691O GLU* 5.7 4.0 - - + -
692O THR 2.2 18.6 + - - +
693O GLU* 1.3 68.2 - - - +
695O THR* 1.3 59.2 + - - +
697O ASN* 3.5 6.1 - - - +
698O LEU* 2.9 21.8 + - - +
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Residues in contact with THR 695 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683O ILE* 4.6 6.5 - - - +
686O GLU* 4.5 8.3 - - - +
687O ILE* 3.8 23.3 - - - -
691O GLU* 3.1 35.6 - - - -
692O THR 2.5 7.1 + - - -
694O ARG* 1.3 73.1 - - - +
696O ARG* 1.3 57.8 + - - -
697O ASN 3.3 0.2 - - - -
698O LEU* 3.2 10.7 + - - +
699O TYR* 2.9 21.7 + - - +
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Residues in contact with ARG 696 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691O GLU 4.1 0.8 + - - -
692O THR* 3.1 11.0 + - - -
693O GLU* 3.0 22.4 - - - +
695O THR* 1.3 75.7 - - - +
697O ASN* 1.3 59.2 + - - +
699O TYR* 3.2 12.5 + - + +
700O ARG* 2.9 22.3 + - - +
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Residues in contact with ASN 697 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693O GLU* 2.6 27.5 + - - +
694O ARG* 3.5 9.4 - - - +
696O ARG* 1.3 76.9 - - - +
698O LEU* 1.3 56.5 + - - +
700O ARG* 2.9 12.0 + - + +
701O ARG* 2.9 26.3 + - - +
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Residues in contact with LEU 698 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683O ILE* 4.6 22.0 - - + +
686O GLU* 6.3 1.6 - - + -
694O ARG 2.9 16.8 + - - +
695O THR* 3.3 15.9 - - - +
696O ARG 3.2 0.4 - - - -
697O ASN* 1.3 75.3 - - - +
699O TYR* 1.3 56.2 + - - +
701O ARG* 3.5 8.0 + - - +
702O LEU* 2.9 25.6 + - - +
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Residues in contact with TYR 699 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683O ILE* 5.7 0.2 - - - +
695O THR 2.9 12.9 + - - +
696O ARG* 3.2 17.4 + - + +
698O LEU* 1.3 77.5 - - - +
700O ARG* 1.3 56.7 + - - +
702O LEU* 3.4 9.7 + - + +
703O LEU* 2.9 24.9 + - - +
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Residues in contact with ARG 700 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696O ARG 2.9 12.5 + - - +
697O ASN* 2.9 17.0 + - + +
699O TYR* 1.3 74.4 - - - +
701O ARG* 1.3 58.1 + - - +
703O LEU* 3.2 10.7 + - - +
704O GLN* 2.9 22.7 + - - +
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Residues in contact with ARG 701 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697O ASN 2.9 11.3 + - - +
698O LEU* 3.5 10.7 + - - +
700O ARG* 1.3 72.7 - - - +
702O LEU* 1.3 60.8 + - - +
703O LEU 3.0 1.3 - - - -
704O GLN* 2.8 25.0 + - + +
705O ARG* 2.9 14.9 + - - +
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Residues in contact with LEU 702 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698O LEU 2.9 18.6 + - - +
699O TYR* 3.5 12.1 - - + +
701O ARG* 1.3 75.8 - - - +
703O LEU* 1.3 56.0 + - - +
705O ARG* 3.7 3.5 - - - +
706O THR* 2.8 32.8 + - - +
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Residues in contact with LEU 703 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699O TYR 2.9 14.5 + - - +
700O ARG* 3.3 13.9 - - - +
701O ARG 3.0 0.4 - - - -
702O LEU* 1.3 74.6 - - - +
704O GLN* 1.3 62.8 + - - +
706O THR* 3.2 17.6 + - - +
713O ILE* 4.8 16.6 - - + -
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Residues in contact with GLN 704 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700O ARG 2.9 11.0 + - - +
701O ARG* 2.8 19.6 + - + +
703O LEU* 1.3 78.6 - - - +
705O ARG* 1.3 56.0 + - - +
706O THR* 3.2 1.3 - - - -
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Residues in contact with ARG 705 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678O LEU* 5.1 16.4 - - + -
701O ARG 2.9 12.2 + - - +
702O LEU* 4.4 4.5 - - - +
704O GLN* 1.3 74.9 - - - +
706O THR* 1.3 71.6 + - - +
707O GLN 3.6 0.2 + - - -
708O HIS* 3.7 10.6 + - - +
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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