Contacts of the strand formed by residues 400 - 406 (chain A) in PDB entry 4WXS
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 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A SER* 2.6 23.2 + - - -
397A ALA* 3.2 17.8 + - + +
398A LYS* 3.2 4.7 + - + +
399A GLY* 1.3 78.7 - - - +
401A ILE* 1.3 63.9 + - - +
402A VAL* 3.3 7.8 + - - +
419A THR 3.5 23.1 - - - +
420A ASN* 4.3 3.1 - - - -
421A ILE 3.1 21.1 - - - +
422A ARG* 4.0 1.5 - - - +
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Residues in contact with ILE 401 (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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371A TYR* 5.0 0.9 - - + -
391A ILE* 3.8 22.2 - - + -
392A TYR 3.6 4.3 - - - -
400A ALA* 1.3 71.4 - - - +
402A VAL* 1.3 68.5 + - - +
403A LEU* 4.5 2.0 - - + -
418A GLU* 4.1 0.2 - - - -
419A THR* 2.6 44.9 + - + +
421A ILE* 2.8 19.9 + - + +
423A LYS* 3.5 34.5 - - + -
426A VAL* 4.2 9.9 - - + -
429A ALA* 4.7 8.1 - - + -
436A LEU* 3.8 19.3 - - + -
438A THR* 3.7 31.0 - - + -
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Residues in contact with VAL 402 (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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391A ILE* 3.5 2.6 - - - -
392A TYR* 2.7 65.8 + - + +
393A SER* 4.3 4.9 - - - -
394A THR* 4.5 7.0 - - + +
397A ALA* 3.3 35.0 - - + -
400A ALA 3.7 2.7 - - - +
401A ILE* 1.3 78.8 - - - +
403A LEU* 1.3 63.8 + - - +
416A THR* 3.4 29.4 - - + -
417A TRP 3.4 6.1 - - - +
418A GLU* 4.1 11.0 - - + +
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Residues in contact with LEU 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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389A TRP* 3.9 18.2 - - + -
390A VAL 3.3 8.1 - - - +
391A ILE* 4.7 11.7 - - + -
401A ILE* 4.5 1.1 - - + -
402A VAL* 1.3 76.5 - - - +
404A SER* 1.3 61.2 + - - +
416A THR* 3.4 0.2 - - - -
417A TRP* 2.8 58.5 + - + +
419A THR* 3.6 31.0 - - + -
431A ILE* 4.3 11.7 - - + -
436A LEU* 4.3 20.2 - - + -
453A TYR* 4.4 4.7 - - + -
455A THR* 3.4 30.3 - - + -
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Residues in contact with SER 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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389A TRP* 3.3 6.9 - - - -
390A VAL* 3.0 43.2 + - - +
392A TYR* 2.7 27.9 + - - -
403A LEU* 1.3 71.6 - - - +
405A LYS* 1.3 63.4 + - - +
406A LEU* 3.5 0.4 + - - -
413A LEU* 3.5 21.5 - - - +
415A GLN 3.1 9.0 - - - -
416A THR* 2.8 20.9 + - - +
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Residues in contact with LYS 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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386A ALA* 3.5 41.2 + - - +
387A GLY* 4.1 0.2 - - - -
388A LEU 3.4 21.8 - - - +
389A TRP* 3.5 30.4 - - + +
404A SER* 1.3 72.7 - - - +
406A LEU* 1.3 61.3 + - - +
413A LEU* 3.6 4.2 - - - -
414A GLU* 2.8 48.7 + - + +
415A GLN* 2.8 19.3 + - + +
417A TRP* 4.0 18.4 - - + -
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Residues in contact with LEU 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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344A VAL* 5.0 2.2 - - + -
360A ILE* 4.5 9.4 - - + -
381A LEU* 4.1 11.4 - - + -
388A LEU* 2.9 49.2 + - + +
389A TRP 4.4 0.2 - - - +
390A VAL* 3.9 36.8 - - + +
404A SER 4.1 1.3 - - - +
405A LYS* 1.3 78.1 - - - +
407A ASN* 1.3 64.5 + - - +
408A PRO* 3.4 9.0 - - - +
411A LEU* 3.5 33.7 - - + +
412A GLU 3.6 1.6 - - - +
413A LEU* 3.6 28.7 - - + -
414A GLU* 4.1 8.6 - - - +
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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