Contacts of the strand formed by residues 402 - 409 (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 GLN 402 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A PHE* 3.7 2.3 - - - +
276A TRP* 2.8 44.5 + - + +
395A SER* 2.9 25.9 + - - +
396A ASN 5.1 0.4 - - - +
397A SER* 3.5 25.1 + - - +
400A GLY 3.6 3.3 + - - +
401A ALA* 1.3 78.8 - - - +
403A HIS* 1.3 64.8 + - - +
98B PRO* 3.5 24.3 - - - +
99B PRO* 3.2 42.5 - - + +
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Residues in contact with HIS 403 (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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226A HIS* 3.3 27.9 + + - -
227A ILE* 3.7 29.1 - - + +
228A GLY 4.8 2.4 + - - -
273A VAL* 4.4 1.7 - - + +
274A LYS 3.2 12.3 - - - +
275A PHE* 3.7 19.7 - - + -
276A TRP* 4.0 3.9 - - - -
401A ALA 5.4 2.5 - - - -
402A GLN* 1.3 80.5 - - - +
404A HIS* 1.3 61.2 + - - +
405A ILE* 3.9 27.0 + - + +
99B PRO* 4.5 8.2 - - - +
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Residues in contact with HIS 404 (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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240A GLU* 4.6 4.7 - - - -
272A LEU 3.9 0.5 - - - +
273A VAL* 3.3 4.5 - - - +
274A LYS* 2.8 35.5 + - + +
276A TRP* 3.5 24.0 - - + -
403A HIS* 1.3 74.8 - - - +
405A ILE* 1.3 62.1 + - - +
406A TYR* 3.5 27.1 - + + +
94B SER* 3.7 24.2 + - - -
97B LYS 3.5 17.7 - - - -
99B PRO* 3.4 36.0 - - + +
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Residues in contact with ILE 405 (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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196A ILE* 3.2 47.6 - - + -
227A ILE* 4.5 10.5 - - + -
239A LEU* 3.8 24.2 - - + +
240A GLU 4.4 2.8 + - - +
271A PHE* 4.1 19.5 - - + -
272A LEU 3.6 4.9 - - - +
273A VAL* 3.9 21.1 - - + -
388A MET* 6.5 0.2 - - - -
403A HIS* 3.9 29.1 + - + +
404A HIS* 1.3 78.3 - - - +
406A TYR* 1.3 69.3 + - - +
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Residues in contact with TYR 406 (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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239A LEU* 5.2 0.2 - - - -
240A GLU* 3.3 34.5 - - + +
242A VAL* 3.9 24.7 - - + -
271A PHE* 3.4 6.1 - - - +
272A LEU* 2.7 52.2 + - + +
274A LYS* 4.2 3.1 - - + -
404A HIS* 3.5 30.3 - + + +
405A ILE* 1.3 81.6 - - - +
407A ARG* 1.3 62.9 + - - +
92B PRO* 4.0 10.3 - - + -
94B SER* 2.6 33.0 + - - -
95B PHE* 3.0 49.7 + + - -
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Residues in contact with ARG 407 (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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239A LEU* 4.8 18.8 - - + +
240A GLU 2.9 20.4 + - - +
241A SER* 3.1 18.3 - - - -
242A VAL 3.0 23.6 + - - -
267A GLN* 4.8 1.8 + - - +
268A ASN* 3.9 34.2 + - - +
270A PHE 4.0 8.1 - - - +
271A PHE* 4.3 16.7 - - + -
406A TYR* 1.3 73.0 - - - +
408A LEU* 1.3 65.9 + - - +
409A VAL* 4.2 18.4 - - - +
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Residues in contact with LEU 408 (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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242A VAL* 3.6 17.5 - - + +
244A ILE* 4.0 31.4 - - + -
247A ILE* 3.9 27.4 - - + -
258A LEU* 4.2 11.7 - - + -
262A PHE* 3.8 6.3 - - + -
267A GLN* 3.8 17.8 - - - +
270A PHE* 3.2 22.6 + - + +
271A PHE 3.5 25.6 - - - +
272A LEU* 3.7 30.5 - - + +
387A CYS* 6.0 0.2 - - - -
389A ALA* 4.5 0.9 - - + -
406A TYR 3.7 0.2 + - - -
407A ARG* 1.3 77.1 + - - +
409A VAL* 1.3 64.3 + - - +
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Residues in contact with VAL 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A SER* 3.9 27.6 - - - +
242A VAL 3.0 19.5 + - - +
243A ASP* 3.3 5.7 - - + +
244A ILE* 2.7 32.6 + - - +
262A PHE* 4.0 9.4 - - - -
267A GLN* 6.1 0.9 - - - -
407A ARG* 4.1 21.1 - - - +
408A LEU* 1.3 81.1 - - - +
410A LYS* 1.3 63.0 + - - +
411A ASP* 4.7 12.3 - - - +
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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