Contacts of the helix formed by residues 479 - 487 (chain F) in PDB entry 7KHC
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 479 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476F ARG* 4.9 9.9 - - - +
477F GLU* 3.4 8.0 + - - -
478F PRO* 1.3 72.3 - - - +
480F PRO* 1.3 71.2 - - - +
481F GLU* 3.3 21.0 + - + +
482F GLU* 2.5 45.6 + - + +
483F LEU* 3.0 8.8 + - - +
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Residues in contact with PRO 480 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041C ASP* 5.6 7.9 - - - +
477F GLU* 5.4 1.1 - - - +
478F PRO 3.8 2.2 - - - +
479F THR* 1.3 89.6 - - - +
481F GLU* 1.3 62.9 + - - +
483F LEU* 3.7 13.9 - - + +
484F ALA* 2.9 28.9 + - - +
491F GLU* 3.7 5.4 - - + +
494F ILE* 4.4 15.0 - - + +
495F ARG* 4.2 23.3 - - + +
498F LEU* 5.8 5.8 - - + -
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Residues in contact with GLU 481 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937C ASP* 2.8 43.4 - - - +
938C GLY* 5.4 0.9 - - - -
479F THR* 2.8 26.8 + - + +
480F PRO* 1.3 81.3 - - - +
482F GLU* 1.3 56.9 + - - +
484F ALA* 3.2 4.0 + - - +
485F GLU* 2.9 26.5 + - - +
491F GLU* 3.8 18.2 - - - +
495F ARG* 5.6 5.0 + - - -
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Residues in contact with GLU 482 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470F MET* 4.5 19.0 - - + +
474F MET* 4.7 9.7 - - + +
476F ARG* 6.2 0.2 - - - +
478F PRO* 4.0 17.0 - - + -
479F THR* 2.5 32.6 + - + +
481F GLU* 1.3 74.9 - - - +
483F LEU* 1.3 56.2 + - - +
485F GLU* 2.7 37.3 + - - +
486F ARG* 2.9 24.7 + - + +
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Residues in contact with LEU 483 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463F LEU* 3.8 32.5 - - + +
466F ILE* 5.0 12.4 - - + +
467F SER* 5.1 9.6 - - - +
477F GLU* 5.1 1.6 - - - +
478F PRO* 2.9 46.0 - - + +
479F THR 3.0 16.7 + - - +
480F PRO* 3.7 10.1 - - + +
482F GLU* 1.3 76.4 - - - +
484F ALA* 1.3 62.5 + - - +
486F ARG* 3.0 17.9 + - - +
487F MET* 3.1 13.3 + - - +
494F ILE* 3.7 20.5 - - + +
498F LEU* 5.9 6.3 - - + -
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Residues in contact with ALA 484 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480F PRO 2.9 9.6 + - - +
481F GLU 3.4 4.5 - - - +
483F LEU* 1.3 75.4 - - - +
485F GLU* 1.3 55.0 + - - +
487F MET 2.3 25.3 - - - +
488F LEU* 4.7 0.3 - - - -
489F MET 3.9 8.7 - - - +
490F PRO 5.1 0.2 - - - -
491F GLU* 2.9 48.5 - - + +
494F ILE* 3.4 10.4 - - - +
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Residues in contact with GLU 485 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481F GLU 2.9 13.2 + - - +
482F GLU* 2.7 39.7 - - - +
483F LEU 3.1 0.2 - - - -
484F ALA* 1.3 75.2 - - - +
486F ARG* 1.3 68.3 + - - +
487F MET 3.1 7.6 + - - +
488F LEU* 5.2 4.0 - - - +
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Residues in contact with ARG 486 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466F ILE* 3.4 45.8 - - + +
469F GLN* 5.4 5.5 + - - -
470F MET* 3.9 29.0 - - + +
482F GLU* 2.9 16.7 + - - +
483F LEU* 3.0 8.2 + - - +
485F GLU* 1.3 79.3 - - - +
487F MET* 1.3 61.3 + - - +
488F LEU* 4.8 5.2 - - - +
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Residues in contact with MET 487 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462F LYS* 3.8 38.4 - - + +
463F LEU* 6.5 1.1 - - + -
466F ILE* 4.1 24.5 - - + -
483F LEU 3.1 10.8 + - - +
484F ALA* 2.3 33.1 - - - +
485F GLU 3.2 4.4 - - - +
486F ARG* 1.3 81.4 - - - +
488F LEU* 1.3 78.3 + - - +
489F MET* 3.3 39.3 + - + +
494F ILE* 5.6 2.9 - - + -
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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