Contacts of the strand formed by residues 326 - 335 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ASN* 3.5 37.1 + - - +
275A THR* 4.6 1.3 - - - +
322A THR* 3.3 1.7 - - - -
323A ILE 2.8 39.3 + - - +
324A ASP 3.2 1.0 + - - -
325A TYR* 1.3 78.8 - - - +
327A GLU* 1.3 69.2 + - - +
328A ILE* 3.4 26.8 + - + -
406A PEG 5.7 0.7 - - - -
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Residues in contact with GLU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A PRO* 5.2 3.5 - - - +
320A LYS* 4.1 30.1 - - + +
321A VAL 3.8 1.7 + - - -
322A THR* 2.5 43.3 + - - +
325A TYR 5.0 1.3 - - - +
326A THR* 1.3 75.7 + - - +
328A ILE* 1.3 66.4 + - - +
329A SER* 3.8 4.4 + - - -
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Residues in contact with ILE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A THR* 4.0 29.8 - - + -
276A VAL* 3.8 25.8 - - + -
319A VAL 3.5 1.0 - - - +
320A LYS* 3.5 3.5 - - - -
321A VAL 2.8 36.5 + - - +
323A ILE* 4.0 14.6 - - + -
326A THR* 3.6 26.7 - - + -
327A GLU* 1.3 72.2 - - - +
329A SER* 1.3 71.8 + - - +
330A PHE* 3.7 25.5 + - + -
344A PRO* 4.3 2.2 - - + -
345A LYS 4.1 7.6 - - - +
346A LEU* 6.4 0.9 - - + -
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Residues in contact with SER 329 (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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318A VAL* 3.9 11.5 - - - +
319A VAL 3.5 4.0 - - - -
320A LYS* 3.5 25.5 + - - +
327A GLU 3.8 4.0 + - - -
328A ILE* 1.3 74.0 - - - +
330A PHE* 1.3 60.0 + - - +
344A PRO* 3.6 1.9 - - - +
345A LYS* 2.9 55.4 + - - +
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Residues in contact with PHE 330 (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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296A ILE* 4.3 12.8 - - + -
298A LEU* 4.7 7.4 - - + -
303A PHE* 4.6 10.8 - + - -
306A ILE* 5.6 2.0 - - + -
318A VAL* 3.4 5.9 - - - +
319A VAL* 2.7 37.9 + - + +
321A VAL* 3.7 30.3 - - + -
323A ILE* 3.9 19.5 - - + -
328A ILE* 3.7 19.3 - - + -
329A SER* 1.3 79.0 - - - +
331A MET* 1.3 62.0 + - - +
332A LEU 3.9 0.2 + - - -
342A PHE* 3.4 42.4 - + + -
343A TYR* 3.2 10.1 - - - +
344A PRO* 3.4 38.8 - - + -
345A LYS* 5.1 0.4 - - - -
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Residues in contact with MET 331 (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 SER* 4.4 5.2 - - - +
317A LYS* 3.7 23.1 - - - +
318A VAL* 3.7 27.1 - - + -
330A PHE* 1.3 71.9 - - - +
332A LEU* 1.3 58.0 + - - +
333A TRP* 3.9 25.6 - - + +
341A THR 3.9 0.7 - - - +
342A PHE* 3.1 7.8 - - - -
343A TYR* 2.9 65.3 + - + +
345A LYS* 3.8 30.5 - - + +
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Residues in contact with LEU 332 (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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307A ILE* 5.2 3.6 - - + -
310A GLN* 3.8 22.7 - - + -
311A ASP 3.6 23.8 - - - +
312A LEU* 4.1 5.2 - - + -
314A VAL 4.9 1.0 - - - +
315A VAL 3.7 0.3 - - - +
316A SER* 3.2 5.4 - - - -
317A LYS* 2.9 41.6 + - + +
319A VAL* 3.9 20.9 - - + -
330A PHE 3.9 0.4 + - - -
331A MET* 1.3 71.9 - - - +
333A TRP* 1.3 64.6 + - - +
334A CYS* 3.8 18.8 - - - -
339A VAL* 4.2 15.5 - - + -
341A THR 3.7 7.9 - - - +
342A PHE* 3.7 25.6 - - + -
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Residues in contact with TRP 333 (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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315A VAL* 3.1 22.9 - - + -
316A SER* 3.6 30.3 - - - -
331A MET* 3.9 19.3 - - + +
332A LEU* 1.3 77.4 - - - +
334A CYS* 1.3 58.8 + - - +
339A VAL* 3.7 1.4 - - - +
340A GLU* 2.7 40.6 + - + +
341A THR* 2.9 41.2 + - + +
343A TYR* 3.4 29.5 + + - -
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Residues in contact with CYS 334 (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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311A ASP 4.8 0.2 - - - -
312A LEU* 3.4 57.9 - - - +
314A VAL 3.5 12.1 - - - +
315A VAL* 2.9 22.1 + - - +
332A LEU* 3.8 18.2 - - - -
333A TRP* 1.3 80.5 - - - +
335A LYS* 1.3 62.7 + - - +
338A HIS 3.2 12.8 - - - +
339A VAL* 4.3 2.2 - - - -
340A GLU* 4.0 6.5 - - - +
404A EDO 3.5 12.2 - - - +
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Residues in contact with LYS 335 (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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334A CYS* 1.3 75.6 - - - +
336A ASP* 1.3 90.0 + - - +
337A GLY 3.2 1.6 - - - -
338A HIS* 2.9 39.6 + - + +
340A GLU* 3.6 32.8 - - + +
404A EDO 3.8 5.4 - - - +
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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