Contacts of the strand formed by residues 334 - 342 (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 334 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298C GLU* 3.0 5.7 - - - +
299C SER 2.7 43.0 + - - +
300C SER 3.7 10.5 - - - -
301C GLU* 3.1 25.8 - - - +
302C ASN* 3.2 38.6 - - + -
327C ALA* 3.7 20.6 - - + -
328C ARG* 3.6 2.5 - - - +
329C PHE* 3.6 46.2 - + + -
333C ARG* 1.3 73.0 - - - +
335C VAL* 1.3 59.8 + - - +
336C TYR* 3.5 5.1 - - - +
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Residues in contact with VAL 335 (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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296C GLN* 3.5 31.2 - - + +
297C TYR 3.4 3.6 - - - +
298C GLU* 4.4 3.1 - - + +
326C TYR 3.9 0.3 - - - +
327C ALA 3.7 0.7 - - - -
328C ARG* 2.8 38.5 + - + +
330C GLU* 3.6 18.2 - - + +
333C ARG* 3.3 37.5 - - + +
334C PHE* 1.3 75.1 - - - +
336C TYR* 1.3 65.5 + - - +
337C ARG* 3.4 32.3 + - + +
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Residues in contact with TYR 336 (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* 4.1 3.8 - - + -
295C SER 3.8 0.9 - - - +
296C GLN* 3.2 3.5 - - - -
297C TYR* 2.7 67.4 + - + +
298C GLU 4.0 0.9 - - - -
299C SER* 3.4 18.8 - - - -
301C GLU 2.9 25.1 + - - -
303C MET* 3.4 29.1 + - - +
305C VAL* 3.4 36.1 - - + -
325C GLU* 3.8 15.0 - - + -
326C TYR 3.4 21.1 - - - -
327C ALA* 3.5 10.7 - - + +
334C PHE 3.5 19.7 - - - -
335C VAL* 1.3 74.7 - - - +
337C ARG* 1.3 62.3 + - - +
338C ILE 3.9 0.6 + - - -
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Residues in contact with ARG 337 (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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295C SER 3.6 4.3 - - - +
296C GLN* 3.2 34.1 + - + +
325C GLU* 3.4 19.0 + - - +
328C ARG* 5.1 17.5 - - - +
330C GLU* 2.9 40.5 + - - -
333C ARG* 5.2 1.0 - - - +
335C VAL* 3.4 21.3 + - + +
336C TYR* 1.3 73.8 - - - +
338C ILE* 1.3 63.6 + - - +
339C ASN* 3.6 19.6 + - + +
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Residues in contact with ILE 338 (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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293C VAL 4.7 2.0 - - - +
294C THR* 3.4 5.9 - - - +
295C SER* 2.8 55.8 + - - +
297C TYR* 4.1 7.4 - - + +
307C CYS* 3.8 30.1 - - + -
321C LYS* 5.7 0.2 - - - +
323C GLU* 3.6 32.1 - - + +
325C GLU* 3.6 28.5 - - + +
336C TYR 3.9 0.4 + - - -
337C ARG* 1.3 70.0 - - - +
339C ASN* 1.3 59.5 + - - +
341C SER* 3.8 26.7 - - - -
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Residues in contact with ASN 339 (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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294C THR* 3.8 13.0 + - - +
337C ARG* 3.6 22.2 + - + +
338C ILE* 1.3 75.1 - - - +
340C ARG* 1.3 89.3 + - - +
341C SER* 3.4 2.9 + - - -
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Residues in contact with ARG 340 (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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209C PHE* 4.0 17.6 - - + -
211C GLU* 2.8 44.8 + - - -
221C LYS* 5.2 2.4 - - - +
290C PHE* 3.5 37.4 - - + +
293C VAL 3.7 2.4 + - - -
294C THR* 3.1 18.7 + - - +
339C ASN* 1.3 88.5 - - - +
341C SER* 1.3 60.9 + - - +
342C PRO* 3.7 4.2 - - - +
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Residues in contact with SER 341 (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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292C GLY* 3.2 0.6 - - - -
293C VAL* 2.7 45.7 + - - +
321C LYS* 2.9 18.6 + - - -
323C GLU* 3.2 4.7 + - - -
338C ILE* 3.8 23.6 - - - -
339C ASN 3.4 1.5 + - - -
340C ARG* 1.3 73.4 - - - +
342C PRO* 1.3 65.2 - - - +
53D GLN* 2.6 27.5 + - - -
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Residues in contact with PRO 342 (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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290C PHE* 3.7 21.8 - - + -
291C TYR 3.4 8.5 - - - +
321C LYS* 4.3 6.4 - - - +
340C ARG 3.7 5.6 - - - +
341C SER* 1.3 83.8 + - - +
343C MET* 1.3 69.2 + - - +
344C P1L 3.7 1.0 + - - -
52D HIS* 5.6 8.3 - - + +
53D GLN* 3.3 40.7 + - + +
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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