Contacts of the strand formed by residues 402 - 409 (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 GLN 402 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C PHE* 3.6 2.3 - - - +
276C TRP* 2.7 65.2 + - + +
395C SER* 4.4 9.4 + - - +
397C SER* 4.3 11.8 + - - +
400C GLY* 3.8 21.3 - - - +
401C ALA* 1.3 76.6 + - - +
403C HIS* 1.3 59.1 + - - +
98D PRO* 3.7 16.4 - - + -
99D PRO* 3.5 41.3 + - + +
100D GLU* 5.5 0.6 + - - +
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Residues in contact with HIS 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C ARG* 5.1 8.3 - - + -
226C HIS* 3.4 26.3 + + - +
227C ILE* 3.8 27.1 - - + +
228C GLY 4.6 3.7 + - - -
229C HIS 5.8 2.2 + - - -
273C VAL* 4.5 3.1 - - + -
274C LYS 3.3 4.3 - - - +
275C PHE* 3.8 26.5 - - + -
276C TRP* 4.6 0.7 - - - -
401C ALA 4.7 7.4 - - - -
402C GLN* 1.3 77.2 - - - +
404C HIS* 1.3 65.9 + - - +
405C ILE* 3.9 29.0 + - + +
99D PRO* 4.7 5.6 - - - +
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Residues in contact with HIS 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C GLU* 5.7 1.3 - - - -
272C LEU 3.8 0.7 - - - +
273C VAL* 3.3 5.2 - - - +
274C LYS* 2.8 35.3 + - + +
276C TRP* 3.4 18.0 - + + -
403C HIS* 1.3 72.4 - - - +
405C ILE* 1.3 63.6 + - - +
406C TYR* 3.6 26.7 + + + +
94D SER* 3.3 30.4 + - - -
97D LYS 3.2 26.5 - - - -
99D PRO* 3.4 30.6 - - + +
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Residues in contact with ILE 405 (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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194C ARG* 4.0 26.9 - - + +
196C ILE* 3.9 33.4 - - + -
239C LEU* 3.5 33.2 - - + +
240C GLU* 4.5 1.9 + - - +
271C PHE* 4.0 23.8 - - + -
272C LEU 3.7 1.8 - - - +
273C VAL* 4.0 17.5 - - + -
403C HIS* 3.9 31.4 + - + +
404C HIS* 1.3 78.9 - - - +
406C TYR* 1.3 71.3 - - - +
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Residues in contact with TYR 406 (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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239C LEU* 4.8 0.7 - - - -
240C GLU* 3.5 32.8 - - + +
242C VAL* 4.0 26.5 - - + -
271C PHE* 3.3 10.2 - - - -
272C LEU* 2.7 54.5 + - + +
274C LYS* 4.3 2.2 - - + -
404C HIS* 3.6 31.5 + + + -
405C ILE* 1.3 77.8 - - - +
407C ARG* 1.3 59.7 + - - +
92D PRO* 4.0 11.4 - - + -
94D SER* 2.4 37.8 + - - -
95D PHE* 3.0 47.4 + + + -
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Residues in contact with ARG 407 (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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194C ARG* 5.5 2.6 - - - +
197C GLY 5.3 3.8 + - - -
239C LEU* 4.5 24.4 + - + +
240C GLU 2.9 14.6 + - - +
241C SER* 3.1 15.6 - - - +
242C VAL 2.9 24.4 + - - -
267C GLN 5.3 2.9 - - - +
268C ASN* 4.1 31.8 + - - +
270C PHE 4.1 8.5 - - - +
271C PHE* 4.2 23.5 - - + -
406C TYR* 1.3 69.5 - - - +
408C LEU* 1.3 72.9 + - - +
409C VAL* 4.3 9.4 - - + -
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Residues in contact with LEU 408 (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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242C VAL* 3.5 24.5 - - + +
244C ILE* 4.0 40.6 - - + -
247C ILE* 5.2 6.5 - - + -
258C LEU* 4.8 5.8 - - + -
262C PHE* 3.8 6.2 - - + -
267C GLN* 3.6 19.6 - - - +
270C PHE* 3.2 25.8 + - + +
271C PHE 3.5 34.3 - - - +
272C LEU* 3.8 20.2 - - + +
387C CYS* 6.1 0.4 - - - -
389C ALA* 4.4 10.5 - - + -
406C TYR 3.6 0.2 + - - -
407C ARG* 1.3 74.5 - - - +
409C VAL* 1.3 61.1 + - - +
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Residues in contact with VAL 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C SER* 3.8 32.8 - - - +
242C VAL 3.0 16.4 + - - +
243C ASP* 3.2 7.0 - - + +
244C ILE* 2.8 30.4 + - - +
262C PHE* 4.1 4.3 - - - -
267C GLN* 5.1 3.1 - - - +
407C ARG* 4.1 12.8 - - + +
408C LEU* 1.3 80.1 - - - +
410C LYS* 1.3 67.3 + - - +
411C ASP* 6.2 0.7 - - - +
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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