Contacts of the strand formed by residues 440 - 446 (chain A) in PDB entry 1ZY7
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 VAL 440 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A MET* 3.7 31.6 - - + -
358A THR 3.4 4.5 - - - +
359A THR* 4.3 16.4 - - + +
425A ILE* 4.3 20.2 - - + -
436A LEU* 3.8 30.5 - - + +
437A LYS* 3.3 34.2 + - + +
438A GLU 3.1 3.3 + - - +
439A ASN* 1.3 76.7 + - - +
441A GLN* 1.3 63.9 + - - +
442A PHE* 4.4 6.5 - - + -
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Residues in contact with GLN 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A LEU* 4.2 25.1 + - - +
316A GLN* 5.3 0.4 - - - +
317A LEU* 4.0 29.6 + - - +
318A HIS* 3.9 15.2 + - - -
357A MET* 3.2 8.0 - - - +
358A THR* 2.9 41.7 + - - +
436A LEU* 5.7 0.2 - - - -
439A ASN* 3.9 12.5 - - - +
440A VAL* 1.3 79.2 - - - +
442A PHE* 1.3 65.4 + - - +
443A HIS* 3.4 21.4 + - - +
541A TYR 5.9 0.2 - - - -
543A SER* 3.2 25.9 + - - +
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Residues in contact with PHE 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A VAL* 4.0 9.4 - - + -
356A VAL 3.5 1.3 - - - -
357A MET* 3.7 34.1 - - + -
369A ILE* 4.2 1.8 - - + -
403A LEU* 3.7 25.1 - - + -
406A PHE* 3.9 9.0 - + - -
407A LEU* 4.1 10.5 - - + -
425A ILE* 3.7 24.2 - - + -
436A LEU* 4.1 20.6 - - + -
440A VAL* 4.4 4.5 - - + -
441A GLN* 1.3 73.6 - - - +
443A HIS* 1.3 63.8 + - - +
528A ILE* 4.5 4.9 - - + -
540A ILE* 3.9 28.7 - - + -
541A TYR 4.7 5.5 + - - +
542A PHE* 3.5 23.1 - - + -
543A SER* 2.8 34.3 + - - +
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Residues in contact with HIS 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A HIS* 4.6 0.7 - - - -
323A LEU* 3.7 18.0 - - + +
327A VAL* 4.1 27.1 - - + +
355A VAL* 3.3 5.9 - - - -
356A VAL* 2.8 51.0 + - + +
358A THR* 2.8 39.8 + - + +
441A GLN* 3.4 27.6 - - + +
442A PHE* 1.3 76.6 + - - +
444A LEU* 1.3 62.9 + - - +
445A TYR 3.9 0.5 + - - -
542A PHE* 4.1 2.9 - - - -
543A SER* 3.9 8.3 - - - -
544A SER* 2.7 37.7 + - - -
546A ILE* 5.2 0.4 - - + -
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Residues in contact with LEU 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A VAL* 4.9 0.7 - - - -
354A GLY 3.6 15.7 - - - +
355A VAL* 4.3 5.6 - - + -
396A GLU* 4.7 16.6 - - + +
399A SER* 4.7 4.0 - - - -
400A ARG 5.7 0.4 - - - +
443A HIS* 1.3 71.0 - - - +
445A TYR* 1.3 61.1 + - - +
446A ILE* 4.1 18.8 - - + -
520A ILE* 4.1 26.7 - - + -
523A TRP* 4.3 7.9 - - + -
542A PHE* 3.9 40.9 - - + -
544A SER 3.0 13.7 + - - +
545A ILE* 3.5 13.7 - - + -
546A ILE* 2.8 35.6 + - - +
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Residues in contact with TYR 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A VAL* 3.7 17.3 - - + -
328A SER* 3.4 35.9 - - - -
331A VAL* 4.0 27.6 - - + -
332A LEU* 6.1 0.7 - - + -
352A LEU* 4.0 19.5 - - + -
353A ALA* 3.1 7.8 - - - +
354A GLY 2.8 34.8 + - - +
443A HIS 3.9 0.4 + - - -
444A LEU* 1.3 73.4 - - - +
446A ILE* 1.3 66.5 + - - +
447A SER* 3.5 27.6 - - - -
546A ILE* 3.3 23.1 - - + -
547A LEU 4.1 1.3 - - - -
548A GLY* 3.3 36.0 - - - -
584A ILE* 4.3 4.5 - - - +
588A GLU* 4.5 8.0 + - - -
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Residues in contact with ILE 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A VAL* 3.8 19.3 - - + -
352A LEU 3.6 4.5 - - - +
353A ALA* 4.5 1.6 - - + -
396A GLU* 3.8 42.4 - - + +
444A LEU* 4.1 13.5 - - + -
445A TYR* 1.3 83.4 - - - +
447A SER* 1.3 61.2 + - - +
448A THR* 3.1 21.7 + - + +
450A PRO* 4.1 14.1 - - + -
520A ILE* 4.0 22.0 - - + -
545A ILE* 4.7 3.4 - - + -
546A ILE 2.9 5.8 + - - +
547A LEU* 3.2 21.2 - - + -
548A GLY 2.8 21.8 + - - -
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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