Contacts of the strand formed by residues 449 - 453 (chain A) in PDB entry 2WOK
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 LEU 449 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A PHE 4.0 0.2 - - - +
307A VAL* 3.2 7.4 - - - -
308A ALA* 2.8 32.7 + - + +
310A GLN* 3.5 28.3 - - + +
395A ILE* 4.6 0.2 - - - -
396A GLY* 3.5 12.8 - - - +
425A LEU* 5.1 1.3 - - + -
430A TYR* 4.5 2.9 - - - +
435A ALA* 4.2 21.8 - - + +
441A VAL* 4.1 19.5 - - + -
446A LEU* 3.7 36.6 - - + +
448A LEU* 1.3 74.3 - - - +
450A VAL* 1.3 64.3 + - - +
451A THR* 4.0 1.2 + - - +
482A LEU* 4.0 31.4 - - + -
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Residues in contact with VAL 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A HIS* 3.5 25.8 - - + -
306A PHE 3.8 3.8 - - - +
307A VAL* 4.5 9.2 - - + +
395A ILE* 3.6 28.0 - - + -
396A GLY 3.1 10.7 + - - +
397A THR* 3.9 14.8 - - - +
402A PHE* 3.7 30.4 - - + +
405A VAL* 4.0 9.0 - - + -
406A ALA* 4.2 8.5 - - + +
430A TYR* 2.7 27.7 + - - -
449A LEU* 1.3 71.2 - - - +
451A THR* 1.3 68.4 + - - +
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Residues in contact with THR 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A HIS* 3.0 18.6 + - - -
306A PHE* 3.0 62.5 + - + +
402A PHE* 3.8 8.3 - - - -
430A TYR* 4.4 3.4 - - - -
431A PHE* 3.1 24.9 - - - -
435A ALA* 5.5 1.6 - - - +
449A LEU* 5.2 1.3 - - - +
450A VAL* 1.3 78.6 - - - +
452A ASP* 1.3 68.0 + - - +
480A TRP* 3.6 13.2 - - + -
482A LEU* 3.8 22.3 - - + +
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Residues in contact with ASP 452 (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 PHE* 4.2 8.2 - - + +
304A LEU 3.3 7.6 - - - -
305A HIS* 2.6 34.3 + - - -
306A PHE* 4.6 0.2 - - - -
338A ARG* 2.7 22.9 + - - -
402A PHE* 3.8 8.4 - - + -
451A THR* 1.3 73.7 + - - +
453A TRP* 1.3 61.1 + - - +
480A TRP* 3.1 21.8 - - - -
529A ASP* 2.6 22.5 - - - +
3B PRO* 3.5 40.2 - - + +
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Residues in contact with TRP 453 (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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139A TYR* 4.6 1.1 - - - -
302A SER 4.2 0.9 - - - +
303A PHE* 3.2 6.6 - - - -
304A LEU* 2.8 36.8 + - + +
306A PHE* 3.7 19.3 - - + -
452A ASP* 1.3 76.2 - - - +
454A GLY* 1.3 68.6 + - - +
455A ALA* 4.0 6.9 - - - +
456A ASP* 4.5 10.3 - - - -
462A GLY 3.6 19.7 - - - -
463A PHE* 2.7 40.4 + + - +
466A PRO* 3.7 26.5 - - + -
467A LEU* 3.8 21.3 - - + -
480A TRP* 3.4 47.6 - + + -
1B ARG* 3.1 37.7 - - - -
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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