Contacts of the strand formed by residues 372 - 376 (chain B) in PDB entry 2WFD
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 ILE 372 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B LEU* 5.2 2.0 - - + -
302B GLN* 4.2 15.3 - - + +
303B THR 3.5 23.1 - - - +
304B ASN* 3.6 30.3 - - - +
361B SER* 3.7 1.2 - - - -
362B LEU* 2.7 60.8 + - + +
364B ALA* 3.6 28.9 - - + +
367B THR* 4.7 2.5 - - + -
369B TYR* 3.7 27.3 + - + +
371B VAL* 1.3 79.0 - - - +
373B TYR* 1.3 64.8 + - - +
426B PHE* 4.1 3.8 - - + -
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Residues in contact with TYR 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B THR 4.6 1.6 + - - -
304B ASN* 3.4 2.6 - - - +
305B CYS 3.2 16.3 + - - -
359B GLY 3.4 20.4 - - - +
360B ALA 3.4 7.2 - - - +
361B SER* 3.3 23.5 + - - -
362B LEU* 4.6 2.5 - - - -
371B VAL* 4.3 18.7 - - + +
372B ILE* 1.3 77.1 - - - +
374B VAL* 1.3 63.7 + - - +
375B LEU* 3.1 24.5 - - + +
419B ARG* 4.4 5.4 + - - -
421B ASP* 3.7 17.6 + - - -
422B MSE 3.5 54.3 - - + +
426B PHE* 4.0 20.6 - + - -
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Residues in contact with VAL 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU* 3.4 31.9 - - + -
305B CYS* 3.8 9.0 - - + -
307B VAL* 4.0 22.2 - - + -
357B ILE* 3.6 26.7 - - + +
358B LEU* 3.7 18.5 - - + +
359B GLY* 3.0 24.9 + - - +
360B ALA* 3.2 13.3 + - + +
362B LEU* 3.4 16.8 - - + -
373B TYR* 1.3 73.3 - - - +
375B LEU* 1.3 66.0 + - - +
418B ILE* 5.1 4.2 - - - +
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ASN* 3.6 22.7 - - + +
305B CYS 3.3 8.9 + - - +
306B TRP* 3.4 21.2 - - + -
307B VAL 3.1 22.5 + - - -
358B LEU* 3.4 7.5 - - - +
373B TYR* 3.1 39.3 - - + +
374B VAL* 1.3 79.3 - - - +
376B PRO* 1.3 68.8 - - + +
403B LEU* 5.7 5.2 - - + -
406B LEU* 3.1 26.9 - - + -
418B ILE* 5.1 6.1 - - + -
422B MSE 4.1 10.5 - - + +
423B VAL* 3.5 22.7 - - + -
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Residues in contact with PRO 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B TRP* 3.1 19.1 - - - -
307B VAL 3.3 7.4 - - - +
309B PRO* 4.3 11.9 - - + -
358B LEU* 3.4 20.4 - - + -
375B LEU* 1.3 88.3 - - + +
377B MSE 1.3 58.5 + - - +
378B LEU* 5.9 3.6 - - + -
406B LEU* 3.8 23.1 - - + +
416B TYR* 4.0 19.5 - - + -
418B ILE* 3.7 27.1 - - + -
454B GLN* 5.1 1.4 - - - +
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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
------------------------------------------------------------
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