Contacts of the strand formed by residues 437 - 443 (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 PHE 437 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A PHE* 3.7 24.2 - + + -
255A SER* 3.6 17.3 - - - -
256A ALA 3.1 27.4 - - - -
307A GLN* 4.9 4.3 - - + -
308A LEU 3.3 15.9 - - - +
309A ILE* 3.9 12.1 - - + -
327A TRP* 3.6 7.8 - - - -
355A TYR* 4.1 22.0 - + - -
356A GLY* 3.4 1.0 - - - -
357A GLN* 3.0 66.5 + - + +
405A TYR* 4.3 2.9 - + - -
420A LEU* 4.5 0.3 - - - +
433A GLY 4.0 9.6 - - - -
434A ASP 3.6 13.5 - - - -
435A VAL 3.9 0.4 - - - -
436A THR* 1.4 81.8 - - - +
438A PHE* 1.3 65.1 + - - +
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Residues in contact with PHE 438 (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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306A LEU 4.3 0.2 - - - +
307A GLN* 3.5 0.8 - - - -
308A LEU* 2.7 44.7 + - + +
327A TRP* 3.6 40.6 - + + -
343A LYS* 5.5 1.3 - - - -
344A ILE* 3.7 21.9 - - + +
354A ILE* 3.9 22.4 - - + -
355A TYR* 3.3 20.2 - - - -
371A ILE* 4.1 14.1 - - + -
418A LEU* 3.8 36.3 - - + -
419A GLN* 3.9 13.5 - - - -
420A LEU* 3.8 23.1 - - + -
437A PHE* 1.3 78.7 - - - +
439A GLY* 1.3 58.9 + - - +
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Residues in contact with GLY 439 (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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306A LEU 3.2 11.7 - - - -
307A GLN* 4.1 0.4 - - - -
344A ILE* 4.1 7.5 - - - +
354A ILE* 3.4 8.3 - - - +
355A TYR* 2.8 57.4 + - - +
438A PHE* 1.3 76.0 - - - +
440A ALA* 1.3 62.7 + - - +
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Residues in contact with ALA 440 (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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258A ILE* 5.1 0.6 - - - +
305A CYS* 3.2 6.1 - - - +
306A LEU 2.9 33.6 + - - +
337A LEU* 3.5 27.8 - - + +
344A ILE* 4.5 5.2 - - + -
352A PHE* 4.6 5.2 - - + -
353A PHE 3.2 9.9 - - - +
354A ILE* 4.2 13.7 - - + -
355A TYR* 3.8 4.9 - - - -
418A LEU* 4.4 9.9 - - + -
439A GLY* 1.3 74.8 - - - +
441A LEU* 1.3 59.2 + - - +
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Residues in contact with LEU 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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56A LEU* 6.3 3.1 - - + -
202A PHE* 5.2 8.7 - - + -
258A ILE* 4.2 15.3 - - + -
290A LEU* 5.8 2.9 - - + -
292A LEU* 3.6 47.3 - - + -
303A GLN* 3.8 26.0 - - + +
304A ASP 3.8 4.9 - - - +
305A CYS* 3.9 10.5 - - + -
352A PHE* 3.2 5.4 - - - -
353A PHE* 2.7 54.0 + - + +
355A TYR* 5.2 0.9 - - + -
440A ALA* 1.3 74.2 - - - +
442A LYS* 1.3 64.1 + - - +
443A LEU* 3.6 10.2 + - + +
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Residues in contact with LYS 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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303A GLN* 3.3 30.6 + - - +
304A ASP* 2.8 31.5 + - + +
336A ALA* 3.5 25.1 - - + -
337A LEU* 4.8 0.2 - - - +
348A GLU* 4.3 11.8 + - - +
349A THR 3.7 23.7 + - - -
350A GLY* 4.4 5.6 - - - -
351A TYR 3.7 9.2 - - - +
352A PHE* 3.8 27.4 - - + -
441A LEU* 1.3 71.8 - - - +
443A LEU* 1.3 71.2 + - - +
444A LEU* 5.0 10.3 - - + +
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Residues in contact with LEU 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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9A VAL* 4.6 5.2 - - + -
36A ARG* 3.9 15.9 + - - +
56A LEU* 6.3 1.6 - - + -
140A VAL* 4.0 33.0 - - + -
303A GLN* 4.4 12.1 - - - +
351A TYR* 2.9 31.6 + - + +
352A PHE 4.4 1.3 - - - -
353A PHE* 4.1 24.2 - - + +
409A ILE* 4.0 38.1 - - + -
441A LEU* 4.1 10.3 - - + +
442A LYS* 1.3 86.0 + - - +
444A LEU* 1.3 68.9 + - - +
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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