Contacts of the strand formed by residues 402 - 412 (chain A) in PDB entry 4ZCH
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 ASN 402 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A ILE 3.5 1.3 - - - -
242A GLN* 3.3 23.2 + - - +
243A ASN* 3.1 44.3 + - - +
359A LEU* 3.4 5.2 - - - +
360A TYR 2.9 28.6 + - - +
393A GLN* 2.9 29.4 + - - +
394A ASN 3.6 22.6 + - - -
395A MET* 3.7 11.7 - - + -
396A PRO* 4.3 1.6 - - - +
401A ASN* 1.3 71.8 - - - +
403A SER* 1.3 59.3 + - - +
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Residues in contact with SER 403 (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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90A ARG* 5.6 0.7 + - - -
240A CYS* 3.8 12.8 - - - -
241A ILE* 2.8 41.8 + - - -
242A GLN* 3.5 14.6 + - - -
254A TYR 5.1 0.9 + - - -
357A GLN* 3.9 24.6 + - - -
358A VAL 3.3 9.0 - - - -
359A LEU* 4.0 8.2 - - - +
393A GLN* 3.1 9.5 - - - +
402A ASN* 1.3 72.0 - - - +
404A CYS* 1.3 60.5 + - - +
405A TYR* 4.0 1.5 + - - +
435A VAL* 4.7 1.6 - - - -
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Residues in contact with CYS 404 (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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102A SER* 4.6 0.2 - - - -
357A GLN* 3.2 2.3 - - - -
358A VAL 2.8 31.3 + - - -
360A TYR* 3.7 15.0 - - + -
368A GLY* 4.6 2.7 - - - -
369A HIS* 3.1 8.6 - - + -
391A CYS* 2.1 48.5 - - + -
392A ILE* 3.4 20.4 - - - -
393A GLN* 3.4 29.6 - - - +
403A SER* 1.3 73.5 - - - +
405A TYR* 1.4 55.9 + - - +
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Residues in contact with TYR 405 (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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60A GLN* 4.4 0.9 - - - +
102A SER* 5.4 0.5 + - - -
104A TYR* 3.3 53.5 + + + +
202A PHE* 4.3 8.7 - - - -
254A TYR* 3.5 27.9 + + + +
256A ALA* 3.3 43.2 + - - +
353A PHE* 4.5 0.9 - - - -
355A TYR* 3.5 29.9 - + + +
356A GLY 3.6 5.6 - - - -
357A GLN* 3.6 33.7 - - + +
391A CYS* 3.4 10.5 - - - -
403A SER 4.0 1.8 + - - -
404A CYS* 1.4 72.4 - - - +
406A SER* 1.3 61.2 + - - +
407A ALA* 3.7 14.6 - - + +
437A PHE* 4.3 3.4 - + - -
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Residues in contact with SER 406 (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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60A GLN* 2.7 26.6 + - - -
104A TYR* 4.2 2.5 - - - -
136A PHE* 3.8 2.6 - - - -
355A TYR* 3.5 1.2 - - - +
356A GLY 3.1 29.9 + - - +
371A ILE* 4.1 11.5 - - - +
389A PHE* 3.7 17.4 - - - +
390A ARG 3.6 10.2 + - - -
391A CYS* 4.0 18.6 - - - -
405A TYR* 1.3 79.4 - - - +
407A ALA* 1.3 63.5 + - - +
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Residues in contact with ALA 407 (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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104A TYR* 3.3 30.7 - - - +
136A PHE* 3.2 26.0 - - - -
353A PHE* 3.5 13.5 - - + -
354A ILE 3.0 15.3 - - - +
355A TYR* 3.7 8.1 - - + -
389A PHE* 4.4 7.4 - - - -
405A TYR* 3.7 13.7 - - + +
406A SER* 1.3 76.7 + - - +
408A GLY* 1.3 58.8 + - - +
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Residues in contact with GLY 408 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A TYR* 3.8 17.7 - - - -
353A PHE* 3.4 11.7 - - - -
354A ILE* 2.8 33.6 + - - +
389A PHE* 3.3 20.2 - - - -
407A ALA* 1.3 77.3 - - - +
409A ILE* 1.3 58.7 + - - -
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Residues in contact with ILE 409 (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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9A VAL* 4.3 12.1 - - + -
10A LEU 4.1 11.0 - - - +
11A HIS* 4.1 13.7 + - + -
34A LEU* 3.9 21.3 - - + +
58A TYR* 3.1 33.2 + - + +
139A PHE 3.6 13.7 - - - +
140A VAL* 3.5 31.9 - - + -
351A TYR* 4.1 15.0 - - + -
352A PHE 3.3 9.0 - - - +
353A PHE* 4.1 4.5 - - + -
389A PHE* 3.4 12.4 - - - -
408A GLY* 1.3 73.7 - - - -
410A ALA* 1.3 66.4 + - - +
443A LEU* 4.0 17.9 - - + -
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Residues in contact with ALA 410 (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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34A LEU* 3.8 9.2 - - - -
351A TYR* 3.3 2.5 - - - -
352A PHE* 2.7 37.8 + - - +
354A ILE* 3.7 22.7 - - + -
373A ARG* 6.2 0.2 - - - +
388A LEU* 4.1 23.1 - - + -
389A PHE* 4.5 2.5 - - + -
409A ILE* 1.3 76.2 - - - +
411A LYS* 1.3 62.7 + - - +
412A LEU* 3.7 10.6 + - + +
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Residues in contact with LYS 411 (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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34A LEU* 3.7 26.1 - - + +
349A THR* 4.0 24.3 - - + +
350A GLY* 3.5 15.3 - - - +
351A TYR* 3.8 35.6 - - + +
373A ARG* 4.7 9.7 + - - -
410A ALA* 1.3 73.3 - - - +
412A LEU* 1.3 64.7 + - - +
413A GLU* 5.1 13.7 - - + +
416A ASP* 4.9 0.9 - - - +
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Residues in contact with LEU 412 (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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346A VAL* 3.9 27.6 - - + -
349A THR* 3.3 4.7 - - - +
350A GLY 2.8 32.7 + - - +
352A PHE* 3.8 27.6 - - + -
354A ILE* 3.8 22.2 - - + -
373A ARG* 3.8 32.1 - - + +
388A LEU* 4.4 2.2 - - + -
410A ALA* 3.7 16.6 + - + -
411A LYS* 1.3 78.9 - - - +
413A GLU* 1.3 62.7 + - - +
416A ASP* 3.8 5.2 - - + +
418A LEU* 4.0 21.5 - - + -
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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