Contacts of the strand formed by residues 343 - 348 (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 THR 343 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A ARG* 4.4 14.4 + - - +
337A GLN* 3.3 5.0 - - - -
338A GLY 2.8 29.8 + - - -
341A SER* 3.2 18.7 + - - -
342A ARG* 1.3 76.5 - - - +
344A VAL* 1.3 73.3 + - - +
345A ILE* 3.9 14.1 + - + -
357A GLU* 4.1 8.7 - - + -
358A LYS 3.6 19.5 - - - +
359A GLU* 2.8 25.3 + - + +
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A TYR* 4.7 4.3 - - + -
336A PHE 3.4 10.8 - - - +
337A GLN* 5.1 2.7 - - + -
342A ARG 3.8 0.6 + - - +
343A THR* 1.3 74.5 - - - +
345A ILE* 1.3 66.8 + - - +
357A GLU* 3.4 1.6 - - - -
358A LYS 2.9 35.3 + - - +
360A ILE* 3.6 32.1 - - + -
379A ILE* 4.4 17.5 - - + -
381A LEU* 4.3 30.1 - - + -
406A LEU* 5.0 1.8 - - + -
411A LEU* 3.3 28.9 - - + +
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Residues in contact with ILE 345 (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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320A ARG* 4.0 20.2 - - + +
334A LEU 3.3 2.4 - - - +
335A TYR* 3.3 7.1 - - - +
336A PHE* 2.7 65.4 + - + +
338A GLY* 3.4 38.6 - - - +
343A THR* 4.0 6.7 - - + +
344A VAL* 1.3 81.4 - - - +
346A ARG* 1.3 63.5 + - - +
354A VAL* 3.7 37.2 - - + -
356A ALA 3.6 2.7 - - - +
357A GLU* 3.6 18.6 - - + +
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Residues in contact with ARG 346 (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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331A SER 5.2 5.3 + - - -
333A SER* 2.9 30.4 + - - +
334A LEU 3.6 2.0 - - - -
335A TYR* 3.6 22.8 + - + -
345A ILE* 1.3 72.5 - - - +
347A TYR* 1.3 55.4 + - - +
348A GLU* 4.4 10.9 + - - +
354A VAL* 3.3 6.1 - - - +
355A LYS* 2.8 61.4 + - + +
356A ALA* 2.8 23.4 + - + +
408A PRO 3.3 20.8 + - - -
409A GLU* 3.0 39.5 + - - +
411A LEU* 4.1 5.0 - - + +
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Residues in contact with TYR 347 (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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316A HIS* 3.6 18.5 - + + +
317A ILE 4.4 6.5 + - - -
318A LEU* 3.7 23.1 - - + -
319A PRO* 3.6 30.1 - - + -
333A SER* 4.0 1.8 - - - -
334A LEU* 2.8 42.2 + - + +
336A PHE* 3.9 17.0 - + + -
346A ARG* 1.3 73.2 - - - +
348A GLU* 1.3 62.5 + - - +
349A LEU* 3.2 33.7 + - + -
352A GLU* 3.1 47.4 - - - +
353A THR 3.5 5.4 - - - -
354A VAL* 4.1 13.9 - - + +
604A GOL 4.6 0.7 - - - -
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Residues in contact with GLU 348 (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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332A GLY* 4.0 8.3 - - - +
333A SER* 3.5 13.3 + - - +
346A ARG* 4.0 10.1 + - - -
347A TYR* 1.3 68.0 - - - +
349A LEU* 1.3 56.4 + - - +
350A ASN* 4.5 4.3 - - + +
351A THR* 2.4 41.2 + - - +
352A GLU* 2.6 37.6 + - - -
353A THR 2.7 15.6 + - - +
355A LYS* 3.0 35.4 + - + +
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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