Contacts of the strand formed by residues 431 - 436 (chain A) in PDB entry 1KYO
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 ALA 431 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU* 3.5 22.3 - - + +
166A THR* 4.6 1.3 - - + -
167A ALA* 3.8 27.6 - - + +
243A PHE* 3.8 13.0 - - + -
244A LEU 4.7 1.6 - - - +
246A SER 3.2 8.7 - - - +
262A LEU* 3.4 5.7 - - - +
263A ALA 2.9 30.1 + - - +
430A ILE* 1.3 74.9 - - - +
432A ILE* 1.3 61.5 + - - +
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Residues in contact with ILE 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 4.5 1.3 - - - -
166A THR* 3.9 2.9 - - - +
246A SER 3.1 6.7 + - - -
247A GLU* 3.2 20.5 - - + +
248A VAL* 3.1 25.8 + - - +
249A ARG* 4.8 5.2 - - + +
260A ILE* 5.0 5.6 - - + -
261A SER 3.7 5.2 - - - +
262A LEU* 4.4 9.0 - - + -
430A ILE* 3.8 21.3 - - + -
431A ALA* 1.3 79.0 - - - +
433A ALA* 1.3 69.8 + - - +
434A GLY 5.1 0.2 - - - +
441A LEU* 4.0 26.5 - - + -
444A TYR* 3.8 26.2 - - + -
447A ILE* 3.6 28.7 - - + -
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Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A VAL* 3.8 26.7 - - + +
162A HIS* 4.4 2.0 - - + -
163A LEU* 3.9 17.0 - - + +
248A VAL* 3.3 21.3 - - + -
250A LEU* 6.1 0.2 - - + -
260A ILE* 3.3 4.9 - - - +
261A SER 2.8 35.2 + - - +
432A ILE* 1.3 82.1 - - - +
434A GLY* 1.3 59.0 + - - +
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Residues in contact with GLY 434 (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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159A VAL* 4.1 6.8 - - - +
248A VAL* 3.3 8.5 + - - +
249A ARG* 4.7 0.8 - - - +
250A LEU* 2.7 37.9 + - - +
259A TRP 3.2 12.1 - - - -
260A ILE* 4.1 4.5 - - - -
432A ILE* 5.1 0.2 - - - +
433A ALA* 1.3 76.9 - - - +
435A THR* 1.3 58.7 + - - -
438A ILE* 3.4 16.3 - - - +
441A LEU* 5.4 2.7 - - - +
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Residues in contact with THR 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A HIS* 4.1 6.7 - - + -
158A ARG* 3.5 30.5 + - - +
159A VAL* 3.2 26.5 - - + -
250A LEU* 2.9 26.7 + - - -
252A ASP* 4.5 1.2 - - - +
255A LEU* 3.8 7.7 - - + +
258A ALA* 3.5 2.6 - - - -
259A TRP* 2.9 47.8 + - + +
434A GLY* 1.3 75.8 - - - -
436A GLY* 1.3 66.3 + - - +
438A ILE* 3.7 6.9 - - - +
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Residues in contact with GLY 436 (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 LEU 3.6 4.0 + - - -
251A ARG* 3.7 2.3 - - - +
252A ASP 2.8 41.4 + - - +
255A LEU* 3.5 16.6 - - - +
257A LYS 3.6 7.6 - - - -
259A TRP* 4.3 0.7 - - - -
435A THR* 1.3 80.6 + - - +
437A GLN* 1.3 61.6 + - - -
438A ILE* 3.0 11.1 + - - +
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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