Contacts of the helix formed by residues 491 - 501 (chain F) in PDB entry 7KHE
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 491 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480F PRO* 5.1 3.1 - - + +
481F GLU* 4.8 15.0 - - + +
484F ALA* 3.3 32.1 - - + -
489F MET* 3.1 9.9 + - - +
490F PRO* 1.3 77.6 - - - +
492F ASP* 1.3 69.0 + - - +
493F LYS 3.5 1.3 - - - +
494F ILE* 3.7 18.3 + - - +
495F ARG* 3.3 34.3 + - - +
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Residues in contact with ASP 492 (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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490F PRO* 2.9 30.2 + - - +
491F GLU* 1.3 82.9 + - - +
493F LYS* 1.3 104.6 + - - +
494F ILE 3.3 1.4 + - - -
495F ARG* 3.3 26.3 - - - +
496F LYS* 4.0 7.8 + - - +
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Residues in contact with LYS 493 (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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489F MET* 4.2 27.6 - - + -
490F PRO* 4.9 6.1 - - + -
491F GLU* 3.5 0.8 - - - +
492F ASP* 1.3 104.7 + - - +
494F ILE* 1.3 68.1 + - + +
495F ARG 3.4 0.2 - - - -
496F LYS* 3.3 23.0 + - + +
497F VAL* 2.9 31.0 + - + +
40X A 2.8 31.8 + - - -
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Residues in contact with ILE 494 (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* 4.4 21.8 - - + -
480F PRO* 4.4 23.6 - - + +
483F LEU* 4.7 7.9 - - + -
484F ALA* 4.2 13.9 - - + +
487F MET* 4.9 12.3 - - - -
489F MET* 3.5 35.4 - - + -
491F GLU* 3.8 25.8 - - - +
492F ASP 3.2 1.2 - - - -
493F LYS* 1.3 78.8 - - + +
495F ARG* 1.3 59.2 + - - +
497F VAL* 3.0 10.4 + - + +
498F LEU* 2.9 38.8 + - + +
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Residues in contact with ARG 495 (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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936C ARG* 3.4 32.9 - - - +
937C ASP 4.3 15.0 + - - -
938C GLY* 6.0 0.4 - - - -
1044C PRO* 5.5 2.6 - - + +
480F PRO* 5.4 17.2 - - + +
491F GLU* 3.3 28.5 + - - +
492F ASP* 3.3 22.3 + - - +
494F ILE* 1.3 75.7 - - - +
496F LYS* 1.3 68.7 + - + +
498F LEU* 3.2 18.3 + - + +
499F LYS* 2.9 41.7 + - + +
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Residues in contact with LYS 496 (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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47D ARG* 4.7 16.8 - - - +
492F ASP 4.0 12.6 - - - +
493F LYS* 3.3 26.5 + - + +
494F ILE 3.2 0.4 - - - -
495F ARG* 1.3 82.1 - - + +
497F VAL* 1.3 64.1 + - + +
499F LYS* 3.0 18.9 + - + +
500F ILE* 2.9 35.0 + - + +
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Residues in contact with VAL 497 (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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456F MET* 4.4 20.9 - - + -
459F THR* 4.6 16.8 - - + -
460F ILE* 3.3 32.2 - - + +
463F LEU* 4.1 18.6 - - + +
493F LYS* 2.9 25.9 + - + +
494F ILE* 3.0 11.2 + - + +
496F LYS* 1.3 77.0 - - + +
498F LEU* 1.3 61.7 + - - +
500F ILE* 3.3 15.3 + - + +
501F ALA* 3.4 13.0 + - - +
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Residues in contact with LEU 498 (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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1044C PRO* 5.6 11.5 - - + +
463F LEU* 3.5 28.5 - - + -
480F PRO* 4.7 20.9 - - + -
483F LEU* 5.4 5.6 - - + -
494F ILE* 2.9 25.0 + - + +
495F ARG* 3.2 19.9 + - + +
497F VAL* 1.3 78.3 - - - +
499F LYS* 1.3 63.0 + - + +
501F ALA* 3.6 11.3 + - - +
502F LYS* 3.8 14.6 - - - +
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Residues in contact with LYS 499 (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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842C ASP* 4.0 21.6 + - - -
936C ARG* 5.2 1.4 - - - +
1044C PRO* 4.2 18.2 - - + -
1045C GLY* 3.8 30.3 - - - +
258D GLY* 5.8 1.0 - - - +
495F ARG* 2.9 35.6 + - + +
496F LYS* 3.3 17.3 - - + +
498F LEU* 1.3 79.2 - - - +
500F ILE* 1.3 67.2 + - + +
501F ALA 3.1 1.0 + - - -
502F LYS* 3.4 22.1 + - - +
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Residues in contact with ILE 500 (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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46D TYR* 4.2 33.7 - - + +
49D PHE* 6.2 0.7 - - + -
448F ARG* 3.5 11.5 + - - +
452F ILE* 4.2 32.2 - - + +
456F MET* 4.8 15.0 - - + -
460F ILE* 4.7 9.4 - - + -
496F LYS* 2.9 30.9 + - + +
497F VAL* 3.3 10.4 + - - +
499F LYS* 1.3 80.3 - - + +
501F ALA* 1.3 61.5 + - - +
502F LYS 3.1 3.8 + - - +
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Residues in contact with ALA 501 (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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448F ARG* 2.8 26.1 + - - +
460F ILE* 4.2 21.8 - - + -
497F VAL 3.4 9.6 + - - +
498F LEU* 3.9 11.9 - - - +
499F LYS 3.1 2.0 + - - -
500F ILE* 1.3 78.3 - - - +
502F LYS* 1.3 64.9 + - + +
503F GLU* 3.2 3.6 + - - +
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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