Contacts of the strand formed by residues 297 - 305 (chain A) in PDB entry 2VKT
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 LYS 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A SER 4.5 0.2 + - - -
296A MET* 1.3 71.4 - - - +
298A ILE* 1.3 61.7 + - - +
329A ASN* 4.5 8.3 + - - +
330A HIS* 3.2 42.0 + - + +
331A LYS 2.9 22.7 + - - -
550A ASN* 6.0 0.8 - - - +
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Residues in contact with ILE 298 (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 MET 3.7 6.9 + - - +
297A LYS* 1.3 74.1 - - - +
299A CYS* 1.3 63.7 + - - +
300A SER* 3.8 12.1 + - - +
330A HIS* 4.3 4.9 - - - -
331A LYS* 3.5 29.8 - - + +
333A ASN* 3.8 28.7 - - + +
365A ASP* 4.4 4.2 - - - +
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Residues in contact with CYS 299 (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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297A LYS 3.9 1.0 + - - -
298A ILE* 1.3 73.5 - - - +
300A SER* 1.3 64.2 + - - +
301A ILE* 3.8 14.3 + - - -
330A HIS* 4.2 11.4 - - + -
331A LYS 3.0 9.6 + - - +
332A LEU* 3.8 5.4 - - - +
333A ASN 2.9 23.4 + - - +
365A ASP* 3.8 8.5 - - - -
544A LEU* 4.3 16.4 - - + -
547A ALA* 3.6 30.3 - - - -
548A THR* 3.7 26.2 - - + -
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Residues in contact with SER 300 (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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298A ILE* 3.8 8.0 - - - +
299A CYS* 1.3 69.6 - - - +
301A ILE* 1.3 63.0 + - - +
333A ASN* 2.8 34.8 + - - +
335A MET* 4.0 15.5 - - - -
363A LYS* 4.6 15.8 + - - +
364A ALA 3.7 0.7 - - - -
365A ASP* 2.8 47.8 + - - +
366A GLY 3.4 4.3 + - - -
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Residues in contact with ILE 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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299A CYS* 4.1 9.0 - - - -
300A SER* 1.3 76.2 - - - +
302A ALA* 1.3 67.4 + - - +
321A LEU* 4.6 6.3 - - + -
332A LEU* 3.9 20.4 - - + -
333A ASN 3.0 7.2 + - - +
334A LEU* 3.5 21.4 - - + +
335A MET* 2.8 33.9 + - - -
366A GLY* 3.3 30.3 - - - +
368A LEU* 4.5 8.1 - - + -
543A LEU* 4.3 25.4 - - + -
544A LEU* 4.5 11.7 - - + -
547A ALA* 4.1 15.7 - - + -
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Residues in contact with ALA 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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301A ILE* 1.3 75.6 - - - +
303A LEU* 1.3 59.3 + - - +
304A VAL* 3.9 1.1 + - + -
335A MET* 3.3 12.6 - - + +
337A ILE* 3.9 23.8 - - + -
360A LYS 4.6 0.9 - - - +
361A LEU* 4.3 13.2 - - + -
364A ALA* 3.8 22.3 - - + +
366A GLY 3.1 8.4 + - - +
367A ILE* 3.6 4.0 - - + +
368A LEU* 2.9 27.4 + - - +
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Residues in contact with LEU 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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301A ILE 3.9 1.0 + - - -
302A ALA* 1.3 70.3 - - - +
304A VAL* 1.3 60.8 + - - +
305A GLY* 3.5 9.7 + - - +
307A TYR 5.3 1.1 - - - +
314A TYR* 4.1 29.6 - - + -
317A VAL* 4.1 24.9 - - + -
318A PHE 5.9 0.4 - - - +
334A LEU* 4.1 21.1 - - + -
335A MET 2.8 12.7 + - - +
336A TYR* 3.7 27.8 - - + -
337A ILE 2.9 26.7 + - - -
368A LEU* 3.6 13.9 - - + -
370A PRO* 3.6 27.6 - - + -
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Residues in contact with VAL 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 ALA 4.5 2.5 - - - +
303A LEU* 1.3 73.1 - - - +
305A GLY* 1.3 57.2 + - - +
337A ILE* 3.7 15.9 - - + +
339A SER* 3.7 22.4 - - - +
342A LEU* 3.9 20.6 - - + -
361A LEU* 3.8 28.9 - - + -
367A ILE* 4.5 7.9 - - + -
368A LEU 3.0 15.3 + - - +
369A VAL* 4.1 10.8 - - + +
370A PRO* 3.5 15.8 - - - +
381A LYS* 4.0 17.1 - - + -
384A ALA* 4.0 14.1 - - + -
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Residues in contact with GLY 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 LEU* 3.5 9.7 + - - +
304A VAL* 1.3 75.3 - - - +
306A LYS* 1.3 60.5 + - - -
307A TYR 3.7 0.7 - - - -
314A TYR* 3.6 12.1 - - - -
337A ILE 3.0 10.1 + - - +
338A ASP* 4.1 0.3 - - - +
339A SER* 2.8 35.7 + - - -
370A PRO* 4.9 2.2 - - - -
381A LYS* 4.2 13.7 - - - -
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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