Contacts of the strand formed by residues 370 - 378 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C LYS* 5.0 0.9 - - - -
311C VAL* 4.6 5.8 - - + -
312C CYS 3.4 8.3 - - - -
313C SER* 5.6 0.2 - - - -
344C P1L 3.9 10.5 - - + -
346C TYR* 4.6 11.0 - + - -
347C MET* 3.6 31.9 - - + -
350C PHE* 3.5 35.4 - + + -
366C VAL 4.4 2.0 - - - +
367C LEU* 3.2 32.4 + - + +
368C GLU 3.4 1.3 - - - +
369C ASN* 1.3 78.5 - - - +
371C THR* 1.3 74.1 + - - +
372C ILE* 3.8 17.0 - - + -
390C CYS 4.6 0.2 - - - +
391C VAL* 4.9 1.2 - - - +
392C PHE* 3.6 42.1 + + - -
68D LEU* 4.3 13.7 - - + -
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Residues in contact with THR 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C LYS* 2.9 52.0 + - + +
251C PHE* 3.5 20.1 - - + -
311C VAL* 3.7 0.2 - - - -
312C CYS* 2.7 54.7 + - - +
315C GLY* 5.1 0.5 + - - -
369C ASN 5.4 1.3 + - - -
370C PHE* 1.3 85.7 - - - +
372C ILE* 1.3 63.9 + - - +
390C CYS 3.4 14.8 - - - +
391C VAL* 4.2 4.5 - - + -
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Residues in contact with ILE 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C PHE* 3.4 5.0 - - - -
309C THR* 3.6 28.9 - - + -
310C LYS 3.3 8.3 - - - +
311C VAL* 4.2 8.5 - - + -
344C P1L 3.7 33.9 - - + -
347C MET* 4.3 4.7 - - + -
370C PHE* 3.8 25.1 - - + -
371C THR* 1.3 80.1 - - - +
373C LEU* 1.3 64.0 + - - +
374C LEU* 4.6 2.7 - - + +
390C CYS* 2.8 51.5 + - + +
392C PHE* 3.9 18.0 - - + -
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Residues in contact with LEU 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C PHE* 3.6 24.0 - - + -
252C PRO* 4.5 17.9 - - + -
256C GLY 5.9 0.2 - - - +
257C GLY* 5.7 0.7 - - - -
258C LEU* 4.1 22.9 - - + +
261C LEU* 4.8 4.7 - - + -
308C SER 3.5 2.1 - - - +
309C THR* 3.5 1.7 - - - -
310C LYS* 2.8 53.6 + - + +
312C CYS* 4.9 2.7 - - - -
372C ILE* 1.3 74.6 - - - +
374C LEU* 1.3 58.4 + - - +
375C VAL* 3.7 19.1 + - + +
387C CYS* 3.7 25.8 - - - -
388C MET 3.9 8.1 - - - +
389C ALA* 4.0 14.6 - - + -
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Residues in contact with LEU 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C LEU* 5.0 0.4 - - + -
206C PHE* 4.7 20.6 - - + -
297C TYR* 3.5 27.4 - - + +
307C CYS* 4.6 5.8 - - + -
308C SER 3.3 16.8 - - - +
309C THR* 3.6 19.3 - - + +
372C ILE* 4.1 5.1 - - + -
373C LEU* 1.3 72.5 - - - +
375C VAL* 1.3 62.9 + - - +
376C VAL* 4.1 14.1 - - + -
386C LEU* 4.1 1.0 - - + +
387C CYS* 3.3 2.4 - - - -
388C MET* 2.7 73.8 + - + +
390C CYS* 5.0 5.8 - - - -
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Residues in contact with VAL 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C LEU* 4.0 33.0 - - + -
306C THR 3.6 3.5 - - - +
308C SER* 2.8 45.2 + - - +
310C LYS* 5.6 6.5 - - + -
373C LEU* 3.7 30.1 - - + +
374C LEU* 1.3 76.4 - - - +
376C VAL* 1.3 64.5 + - - +
377C THR* 4.0 10.8 + - + +
384C THR* 4.5 11.9 - - + +
386C LEU 3.5 7.9 - - - +
387C CYS* 4.1 6.5 - - + -
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Residues in contact with VAL 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C LEU* 3.5 24.7 - - + -
297C TYR* 3.6 36.8 - - + +
305C VAL* 3.3 34.5 - - + -
306C THR 3.3 5.2 - - - +
307C CYS* 3.9 9.4 - - - -
374C LEU* 4.1 9.6 - - + -
375C VAL* 1.3 72.8 - - - +
377C THR* 1.3 61.4 + - - +
384C THR* 3.9 2.4 - - - +
385C LEU* 2.9 23.5 + - + -
386C LEU* 2.8 31.8 + - + +
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Residues in contact with THR 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C VAL* 3.6 1.4 - - - -
306C THR* 2.7 67.9 + - + +
308C SER* 5.9 2.2 - - - -
375C VAL* 4.3 13.9 - - + +
376C VAL* 1.3 77.3 - - - +
378C ASN* 1.3 70.9 + - - +
379C ARG* 3.3 1.0 + - - -
382C GLN* 3.8 20.7 + - - +
383C GLU 3.2 14.9 + - - -
384C THR* 4.6 3.7 + - - -
385C LEU* 3.8 5.6 - - - +
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Residues in contact with ASN 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C LYS* 6.0 0.4 - - - +
303C MET* 3.3 31.1 - - - +
304C THR 3.7 8.1 - - - +
377C THR* 1.3 68.4 + - - +
379C ARG* 1.3 56.3 + - - +
380C ASP* 3.0 25.5 + - - +
381C THR* 3.2 33.4 + - - +
382C GLN* 2.7 36.4 + - - +
383C GLU* 2.9 19.0 + - + +
385C LEU* 3.4 20.0 - - + +
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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