Contacts of the strand formed by residues 436 - 442 (chain H) in PDB entry 6NZD
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 ALA 436 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367H HIS* 4.4 2.9 - - - -
372H ASN* 4.7 0.7 - - - -
373H GLN* 3.3 22.0 - - + +
375H ILE* 4.5 4.3 - - + -
430H VAL* 4.1 34.1 - - + +
433H SER* 3.7 11.3 + - - +
434H GLU 3.5 0.6 + - - -
435H PHE* 1.3 79.9 - - - +
437H VAL* 1.3 62.9 + - - +
438H ILE* 5.3 1.3 - - + -
469H SER* 2.8 23.4 + - - -
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Residues in contact with VAL 437 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363H MET* 4.1 11.2 - - - -
364H LEU* 4.2 20.0 - - + -
367H HIS* 3.5 36.8 - - + -
373H GLN 3.0 9.4 + - - +
374H VAL* 4.1 12.3 - - + -
375H ILE* 3.0 26.3 + - - +
436H ALA* 1.3 73.3 - - - +
438H ILE* 1.3 70.9 + - - +
439H VAL* 5.5 0.2 - - - -
467H VAL* 3.7 24.5 - - + -
468H THR 3.4 13.0 - - - +
469H SER* 4.2 1.1 - - - -
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Residues in contact with ILE 438 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375H ILE* 3.4 26.9 - - + +
377H LYS* 5.6 2.2 - - + -
426H ILE* 4.5 18.6 - - + -
430H VAL* 4.6 7.0 - - + +
431H LEU* 3.7 41.7 - - + -
436H ALA* 5.3 1.1 - - + -
437H VAL* 1.3 81.1 - - - +
439H VAL* 1.3 68.4 + - - +
440H GLU* 4.0 25.6 - - + +
466H VAL 3.7 1.0 - - - +
467H VAL* 3.4 4.2 - - - +
468H THR* 2.8 51.2 + - - +
469H SER* 6.3 0.2 - - - -
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Residues in contact with VAL 439 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356H LEU* 4.6 2.2 - - + -
364H LEU* 4.3 15.9 - - + -
374H VAL* 5.9 0.2 - - + -
375H ILE 2.7 11.0 + - - +
376H TRP* 3.4 58.3 - - + +
377H LYS* 2.9 27.4 + - - +
437H VAL* 4.9 0.9 - - + -
438H ILE* 1.3 77.0 - - - +
440H GLU* 1.3 67.6 + - - +
441H VAL* 4.4 0.3 - - - +
465H PHE* 4.5 10.5 - - + -
466H VAL 3.5 8.5 - - - +
467H VAL* 4.0 24.0 - - + -
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Residues in contact with GLU 440 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377H LYS* 3.8 35.6 + - + +
426H ILE* 5.2 4.3 - - - +
431H LEU* 5.8 3.6 - - - +
438H ILE* 4.0 17.6 - - + +
439H VAL* 1.3 76.1 - - - +
441H VAL* 1.3 62.5 + - - +
442H HIS* 3.6 30.9 + - + +
464H GLU 3.9 0.5 - - - +
465H PHE* 3.6 2.8 - - - -
466H VAL* 3.0 42.1 + - + +
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Residues in contact with VAL 441 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376H TRP* 4.2 18.4 - - + -
377H LYS 3.0 21.3 + - - +
378H SER* 3.7 26.7 + - - +
379H ARG 5.1 1.6 + - - -
383H LEU* 4.1 7.2 - - + -
439H VAL* 4.4 2.2 - - + +
440H GLU* 1.3 77.5 - - - +
442H HIS* 1.3 73.7 + - - +
463H TYR* 3.9 23.6 - - + -
464H GLU 3.4 10.1 - - - +
465H PHE* 3.9 28.9 - - + -
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Residues in contact with HIS 442 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377H LYS* 6.4 0.2 - - - -
440H GLU* 3.6 33.5 + - + +
441H VAL* 1.3 82.7 + - - +
443H ALA* 1.3 65.4 + - - +
463H TYR* 3.4 11.6 - - - -
464H GLU* 2.8 39.7 + - + +
466H VAL* 5.4 9.2 - - + -
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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