Contacts of the strand formed by residues 370 - 378 (chain A) in PDB entry 3KYS
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 PHE 370 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A VAL* 4.3 12.6 - - + -
312A CYS 3.6 6.7 - - - -
313A SER* 4.8 0.4 - - - +
344A P1L 3.8 9.6 - - + -
346A TYR* 4.5 9.0 - + - -
347A MET* 3.5 29.2 - - + -
350A PHE* 3.5 36.6 - + + -
366A VAL 4.3 0.4 - - - +
367A LEU* 3.1 31.6 + - + +
368A GLU 3.3 1.1 - - - +
369A ASN* 1.3 77.9 - - - +
371A THR* 1.3 72.3 + - - +
372A ILE* 3.7 17.5 - - + -
390A CYS 4.6 0.3 - - - +
391A VAL* 4.8 1.2 - - - +
392A PHE* 3.5 42.9 + + - -
68B LEU* 4.1 16.4 - - + -
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Residues in contact with THR 371 (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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250A LYS* 3.0 41.7 + - + +
251A PHE* 3.6 23.0 - - + -
311A VAL* 3.5 0.9 - - - -
312A CYS* 2.5 57.3 + - - +
314A PHE 4.6 0.3 + - - -
368A GLU 5.2 0.2 - - - +
369A ASN 5.2 0.8 + - - -
370A PHE* 1.3 87.5 - - - +
372A ILE* 1.3 60.9 + - - +
390A CYS 3.4 15.0 - - - +
391A VAL* 4.1 10.5 - - + -
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Residues in contact with ILE 372 (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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251A PHE* 3.4 4.3 - - - -
309A THR* 3.9 25.1 - - + -
310A LYS 3.2 9.9 - - - +
311A VAL* 4.0 13.7 - - + -
344A P1L 3.9 30.1 - - + -
347A MET* 4.6 0.9 - - - -
370A PHE* 3.7 19.7 - - + -
371A THR* 1.3 78.6 - - - +
373A LEU* 1.3 65.4 + - - +
374A LEU* 4.5 3.1 - - + +
389A ALA* 3.7 0.3 - - - -
390A CYS* 2.8 51.7 + - + +
392A PHE* 3.5 27.7 - - + -
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Residues in contact with LEU 373 (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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251A PHE* 4.0 16.6 - - + -
252A PRO* 4.8 3.8 - - + -
257A GLY 5.0 0.7 - - - -
258A LEU* 4.2 30.5 - - + +
261A LEU* 5.1 1.6 - - + -
308A SER 3.6 3.5 - - - +
310A LYS* 2.8 62.6 + - + +
312A CYS* 4.0 10.6 - - - -
372A ILE* 1.3 73.3 - - - +
374A LEU* 1.3 60.3 + - - +
375A VAL* 3.8 18.8 - - + -
387A CYS* 3.7 23.8 - - - -
389A ALA* 3.9 23.6 - - + -
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Residues in contact with LEU 374 (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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203A LEU* 4.7 5.4 - - + -
206A PHE* 4.4 15.9 - - + -
297A TYR* 3.9 24.2 - - + +
307A CYS* 4.8 2.7 - - + -
308A SER 3.5 12.8 - - - +
309A THR* 3.5 30.5 - - + +
372A ILE* 4.0 4.4 - - + -
373A LEU* 1.3 72.3 - - - +
375A VAL* 1.3 61.8 + - - +
376A VAL* 4.2 13.5 - - + -
386A LEU* 4.0 0.8 - - + +
387A CYS* 3.3 3.1 - - - -
388A MET* 2.6 79.0 + - + +
390A CYS* 5.1 1.1 - - - -
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Residues in contact with VAL 375 (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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261A LEU* 4.0 28.3 - - + -
306A THR 3.8 1.7 - - - +
307A CYS* 3.7 0.3 - - - -
308A SER* 2.8 47.3 + - - +
310A LYS* 5.3 5.4 - - + +
373A LEU* 3.8 24.0 - - + -
374A LEU* 1.3 78.9 - - - +
376A VAL* 1.3 61.5 + - - +
377A THR* 3.5 19.6 + - - +
384A THR* 4.5 11.4 - - + +
386A LEU 3.5 7.0 - - - +
387A CYS* 3.9 12.1 - - + -
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Residues in contact with VAL 376 (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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201A LEU* 3.8 28.5 - - + -
297A TYR* 3.8 35.2 - - + +
305A VAL* 3.8 27.1 - - + -
306A THR 3.5 5.8 - - - +
307A CYS* 4.0 11.2 - - + -
374A LEU* 4.6 9.6 - - + -
375A VAL* 1.3 72.0 - - - +
377A THR* 1.3 66.2 + - - +
384A THR* 3.9 1.6 - - - -
385A LEU* 2.8 25.1 + - + -
386A LEU* 2.8 24.7 + - + +
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Residues in contact with THR 377 (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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261A LEU* 6.1 0.2 - - - +
305A VAL* 3.6 1.6 - - - -
306A THR* 2.7 49.7 + - - -
375A VAL* 3.5 20.1 + - - +
376A VAL* 1.3 78.4 + - - +
378A ASN* 1.3 74.6 + - - +
379A ARG* 3.2 1.2 + - - -
382A GLN* 3.6 27.6 - - - +
383A GLU 3.2 16.8 - - - +
384A THR* 4.3 4.0 + - - +
385A LEU* 3.8 5.8 - - - +
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Residues in contact with ASN 378 (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 MET* 3.6 34.9 - - - +
304A THR 3.4 14.8 + - - +
377A THR* 1.3 68.4 - - - +
379A ARG* 1.3 55.8 + - - +
380A ASP* 2.9 21.2 + - - +
381A THR* 3.0 36.9 + - - +
382A GLN* 2.7 36.6 + - - -
383A GLU* 2.9 20.9 + - + +
385A LEU* 3.5 18.1 - - + +
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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