Contacts of the strand formed by residues 326 - 335 (chain B) in PDB entry 6W01
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 326 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B ASN* 3.6 36.9 + - - +
275B THR* 4.4 2.9 - - - +
322B THR* 3.3 4.9 - - - -
323B ILE 2.8 39.5 + - - +
324B ASP 3.2 0.6 - - - -
325B TYR* 1.3 79.4 - - - +
327B GLU* 1.3 63.8 + - - +
328B ILE* 3.5 27.7 + - + -
403B EDO 4.3 10.3 + - - +
411B PEG 5.6 0.2 - - - -
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Residues in contact with GLU 327 (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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320B LYS* 3.4 56.1 + - + +
321B VAL 3.7 4.7 - - - +
322B THR* 4.2 14.6 + - - +
325B TYR 4.4 0.2 + - - -
326B THR* 1.3 76.4 + - - +
328B ILE* 1.3 65.1 + - - +
329B SER* 3.9 3.7 + - - +
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Residues in contact with ILE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B THR* 4.1 7.9 - - + -
276B VAL* 3.9 24.5 - - + -
319B VAL 3.6 0.9 - - - +
320B LYS* 3.4 2.2 - - - -
321B VAL 2.8 37.2 + - - +
323B ILE* 4.1 21.8 - - + -
326B THR* 3.5 28.9 - - + -
327B GLU* 1.3 75.6 - - - +
329B SER* 1.3 69.9 + - - +
330B PHE* 3.6 28.5 - - + -
344B PRO* 4.7 4.3 - - + -
403B EDO 3.7 23.8 - - - -
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Residues in contact with SER 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B VAL* 3.9 16.3 - - - +
319B VAL 3.5 4.9 - - - -
320B LYS* 3.5 26.7 + - - +
327B GLU* 3.9 3.8 + - - +
328B ILE* 1.3 76.1 - - - +
330B PHE* 1.3 55.3 + - - +
344B PRO* 3.5 5.5 - - - +
345B LYS* 2.7 46.2 + - - +
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Residues in contact with PHE 330 (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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296B ILE* 4.6 11.0 - - + -
298B LEU* 5.0 7.0 - - + -
303B PHE* 4.8 10.3 - + - -
306B ILE* 5.7 2.2 - - + -
318B VAL* 3.4 6.2 - - - +
319B VAL* 2.7 41.5 + - + +
321B VAL* 3.9 27.4 - - + -
323B ILE* 4.1 14.6 - - + -
328B ILE* 3.6 32.8 - - + -
329B SER* 1.3 75.0 - - - +
331B MET* 1.3 61.1 + - - +
332B LEU 3.9 0.2 + - - -
342B PHE* 3.5 43.3 - + + -
343B TYR* 3.2 8.3 - - - +
344B PRO* 3.5 35.0 - - + -
345B LYS* 4.4 2.0 - - - -
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Residues in contact with MET 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B SER* 4.6 4.0 - - - +
317B LYS* 3.8 18.8 - - - +
318B VAL* 3.7 26.9 - - + -
330B PHE* 1.3 72.1 - - - +
332B LEU* 1.3 59.4 + - - +
333B TRP* 3.8 29.6 - - + +
341B THR 3.9 0.9 - - - +
342B PHE* 3.1 8.3 - - - -
343B TYR* 2.8 72.7 + - + +
345B LYS* 3.9 27.1 - - + +
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Residues in contact with LEU 332 (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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307B ILE* 5.2 2.0 - - + -
310B GLN* 3.8 29.8 - - + +
311B ASP 3.8 22.0 - - - +
312B LEU* 4.4 2.2 - - + -
314B VAL* 5.2 0.8 - - + +
315B VAL 3.9 0.5 - - - +
316B SER* 3.2 5.5 - - - -
317B LYS* 3.0 45.1 + - + +
319B VAL* 4.2 9.2 - - + -
330B PHE 3.9 0.2 + - - -
331B MET* 1.3 73.0 - - - +
333B TRP* 1.3 65.3 + - - +
334B CYS* 3.8 23.0 - - - -
339B VAL* 4.1 19.3 - - + -
341B THR 3.7 6.5 - - - +
342B PHE* 3.6 25.4 - - + -
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Residues in contact with TRP 333 (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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315B VAL* 3.3 24.9 - - + -
316B SER* 3.5 32.5 - - - -
331B MET* 3.8 18.7 - - + +
332B LEU* 1.3 75.4 - - - +
334B CYS* 1.3 55.8 + - - +
339B VAL* 3.6 3.3 - - - +
340B GLU* 2.6 45.4 + - + +
341B THR* 2.8 43.7 + - + +
343B TYR* 3.3 27.4 + + - -
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Residues in contact with CYS 334 (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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311B ASP 4.6 0.4 - - - -
312B LEU* 3.6 50.9 - - - +
314B VAL* 3.3 20.0 - - - +
315B VAL* 2.9 25.6 + - - +
332B LEU* 3.8 19.5 - - - -
333B TRP* 1.3 78.9 - - - +
335B LYS* 1.3 66.2 + - - +
338B HIS 3.2 13.9 - - - +
339B VAL* 4.3 2.0 - - - -
340B GLU* 3.4 10.3 - - - +
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Residues in contact with LYS 335 (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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315B VAL* 5.9 2.5 - - + -
334B CYS* 1.3 78.1 - - - +
336B ASP* 1.3 92.0 + - - +
337B GLY 3.1 1.9 + - - -
338B HIS* 2.9 40.6 + - + +
340B GLU* 3.7 28.7 - - + +
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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