Contacts of the strand formed by residues 465 - 469 (chain D) 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 GLN 465 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1237C HIS* 6.0 1.0 - - - -
1242C LYS* 3.6 38.9 - - - +
352D ARG* 3.6 34.0 + - - +
353D SER 3.3 13.9 - - - +
354D VAL* 4.3 10.0 - - + +
425D ARG* 4.0 15.8 - - - +
426D ALA* 5.0 2.6 + - - +
463D GLY 3.7 11.2 + - - +
464D ASP* 1.3 80.2 - - - +
466D MET* 1.3 70.1 + - - +
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Residues in contact with MET 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D ARG* 3.1 6.0 - - - -
353D SER 2.9 31.3 + - - +
355D ILE* 3.4 19.3 - - + +
423D LEU* 4.5 16.8 - - + -
424D ASN 3.5 14.1 - - - +
425D ARG* 4.3 8.5 - - + +
447D ILE* 4.1 9.3 - - + +
449D LEU* 3.2 36.1 - - + -
457D TYR* 3.9 28.3 - - + -
459D ALA* 3.4 31.6 - - + -
464D ASP* 6.4 0.2 - - + -
465D GLN* 1.3 79.7 - - - +
467D ALA* 1.3 63.8 + - - +
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Residues in contact with ALA 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1268C GLN* 4.1 16.6 - - + -
351D GLY 3.1 12.6 - - - +
352D ARG* 4.0 2.9 - - + -
422D LEU 3.6 0.2 - - - +
423D LEU* 3.3 6.4 - - - +
424D ASN* 2.9 40.0 + - + +
466D MET* 1.3 74.5 - - - +
468D VAL* 1.3 62.6 - - - +
469D HIS* 3.9 20.4 - - + +
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Residues in contact with VAL 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D TYR 4.2 0.5 - - - +
350D SER* 3.5 3.5 - - - -
351D GLY* 2.8 38.8 + - - +
368D LEU* 4.5 16.4 - - + -
372D MET* 3.7 25.8 - - + -
376D LEU* 4.4 15.9 - - + +
421D VAL* 5.2 3.6 - - + -
422D LEU 3.1 5.2 - - - +
423D LEU* 3.7 29.4 - - + -
447D ILE* 4.0 19.7 - - + -
466D MET 5.4 0.2 - - - -
467D ALA* 1.3 78.3 - - - +
469D HIS* 1.3 63.1 + - - +
470D VAL* 5.3 0.9 - - - -
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Residues in contact with HIS 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1268C GLN* 4.1 11.9 - - + +
1269C ARG 5.1 0.9 - - - -
1270C PHE* 3.0 50.6 - + + -
1290C MET* 4.4 10.0 - - + +
1294C LYS* 5.4 1.1 + - - +
347D VAL* 3.8 9.4 - - + +
348D ASP 5.0 0.2 + - - -
349D TYR 3.7 5.5 + - - +
350D SER* 3.5 28.0 - - - -
421D VAL* 3.5 7.4 - - - +
422D LEU* 2.9 44.7 + - + +
424D ASN* 5.0 9.9 + - + +
467D ALA* 3.9 20.0 - - + +
468D VAL* 1.3 82.4 - - - +
470D VAL* 1.3 64.9 + - - +
471D PRO* 3.9 0.8 - - - +
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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