Contacts of the strand formed by residues 300 - 308 (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 ARG 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A VAL* 5.7 0.4 - - - +
298A ASN 3.9 0.2 + - - -
299A PRO* 1.3 84.9 - - - +
301A THR* 1.3 61.4 + - - +
302A SER* 4.3 9.8 + - - +
346A ASP* 2.7 42.4 + - + +
347A LEU 5.2 0.4 + - - -
354A PRO* 3.3 43.2 - - + +
355A THR* 6.5 1.1 - - + -
359A HIS* 6.3 0.4 - - - -
528A HIS* 3.4 33.4 - - + +
529A ASP 3.5 9.0 - - - +
530A LYS* 4.1 18.1 - - + +
544A VAL* 5.1 0.5 - - - +
549A GLY* 4.0 8.1 - - - -
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Residues in contact with THR 301 (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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300A ARG* 1.3 75.3 - - - +
302A SER* 1.3 54.9 + - - +
303A PHE* 3.2 32.0 + - - +
529A ASP* 3.0 18.8 + - + +
530A LYS 4.3 3.1 - - - -
531A THR* 3.6 40.8 - - + +
548A PHE 5.5 0.7 - - - -
549A GLY* 4.2 15.4 - - - +
550A LEU* 6.1 1.8 - - + -
1562A GOL 2.7 36.8 + - - -
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Residues in contact with SER 302 (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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300A ARG* 3.4 10.4 + - - +
301A THR* 1.3 80.5 - - - +
303A PHE* 1.3 62.6 + - - +
353A PRO* 3.6 31.4 - - - +
355A THR* 3.6 30.2 + - - +
453A TRP 4.2 0.7 - - - +
454A GLY* 4.4 4.0 - - - -
455A ALA 4.8 1.4 + - - -
463A PHE* 3.8 10.2 - - - -
528A HIS* 5.5 3.1 - - - +
529A ASP 4.4 1.4 + - - -
546A PRO 4.5 4.6 + - - -
549A GLY* 5.9 0.3 + - - -
1562A GOL 3.6 16.2 + - - -
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Residues in contact with PHE 303 (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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54A VAL* 4.6 6.1 - - + -
301A THR* 3.2 30.9 + - - +
302A SER* 1.3 79.2 - - - +
304A LEU* 1.3 58.1 + - - +
452A ASP* 4.2 9.6 - - - +
453A TRP 3.2 13.5 - - - -
454A GLY* 3.3 25.6 - - - -
528A HIS* 3.4 7.3 - - - +
529A ASP* 2.9 39.7 + - + +
548A PHE 5.7 0.2 - - - -
1562A GOL 3.7 32.1 - - - -
1B ARG* 3.8 16.6 - - - -
2B PRO 4.1 2.9 - - - -
3B PRO* 3.7 33.9 - - + -
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Residues in contact with LEU 304 (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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302A SER 3.9 0.6 + - - -
303A PHE* 1.3 73.0 - - - +
305A HIS* 1.3 69.0 + - - +
306A PHE* 3.6 28.9 - - + -
348A THR* 3.8 22.0 - - + -
350A ALA 4.2 0.2 - - - +
351A LEU* 3.7 29.6 - - + +
452A ASP* 3.3 3.5 - - - -
453A TRP* 2.8 35.2 + - + +
463A PHE* 3.7 31.4 - - + -
467A LEU* 4.8 4.0 - - + -
525A PRO* 4.1 8.3 - - + -
527A VAL 3.6 15.9 - - - +
528A HIS* 3.8 13.9 - - + +
529A ASP* 4.5 2.0 - - - -
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Residues in contact with HIS 305 (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 0.6 - - - -
304A LEU* 1.3 73.0 - - - +
306A PHE* 1.3 63.5 + - - +
334A LEU 5.8 0.4 - - - -
338A ARG* 3.5 25.1 - - + -
402A PHE* 4.1 11.0 - + - -
405A VAL* 3.3 30.3 - - + +
450A VAL* 3.5 28.7 - - + -
451A THR 3.0 12.7 + - - -
452A ASP* 2.6 26.1 + - - +
526A LEU* 2.9 44.1 + - + +
527A VAL* 2.9 30.0 + - + +
529A ASP* 3.9 7.3 + - - +
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Residues in contact with PHE 306 (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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304A LEU* 3.6 28.7 - - + -
305A HIS* 1.3 76.7 + - - +
307A VAL* 1.3 71.3 + - - +
308A ALA* 4.3 8.3 - - + -
351A LEU* 5.4 0.2 - - + -
449A LEU 4.0 0.2 - - - +
450A VAL* 3.8 2.6 - - - +
451A THR* 3.0 63.1 + - + +
453A TRP* 3.7 24.5 - - + -
467A LEU* 4.1 27.4 - - + -
480A TRP* 5.0 2.7 - + - -
482A LEU* 4.7 5.4 - - + -
523A LEU* 3.6 37.0 - - + -
524A LEU 3.3 16.4 - - - +
525A PRO* 4.0 8.1 - - + -
526A LEU* 4.3 4.9 - - - -
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Residues in contact with VAL 307 (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 PHE* 1.3 81.3 - - - +
308A ALA* 1.3 70.3 + - - +
309A MET* 4.2 2.2 + - + +
395A ILE* 4.7 2.7 - - + -
405A VAL* 5.1 0.7 - - + -
409A VAL* 4.3 20.6 - - + -
448A LEU* 3.8 30.1 - - + -
449A LEU 3.2 12.8 - - - +
450A VAL* 4.5 11.4 - - + -
522A VAL 4.0 0.2 - - - +
523A LEU* 3.6 2.6 - - - -
524A LEU* 2.8 51.3 + - + +
526A LEU* 4.0 20.2 - - + -
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Residues in contact with ALA 308 (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 PHE* 4.1 3.6 - - + -
307A VAL* 1.3 74.3 - - - +
309A MET* 1.3 60.7 + - - +
310A GLN* 3.1 20.7 + - - +
448A LEU* 3.2 4.3 - - - -
449A LEU* 2.8 33.0 + - + +
482A LEU* 3.7 31.6 - - + -
483A PRO* 4.2 1.6 - - + -
522A VAL 3.5 4.9 - - - -
523A LEU* 4.0 16.8 - - + -
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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