Contacts of the strand formed by residues 431 - 436 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163L LEU* 3.5 14.8 - - + +
166L THR* 4.5 0.9 - - + -
167L ALA* 3.5 38.6 - - + +
243L PHE* 3.9 7.1 - - + -
244L LEU 4.9 0.9 - - - +
246L SER 3.1 7.4 - - - +
262L LEU* 3.2 6.8 - - - +
263L ALA 2.7 38.1 + - - +
430L ILE* 1.3 74.5 - - - +
432L ILE* 1.3 63.0 + - - +
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Residues in contact with ILE 432 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163L LEU* 3.8 1.6 - - - -
166L THR* 3.9 2.1 - - - +
246L SER 3.1 5.5 + - - -
247L GLU* 3.2 18.3 - - + +
248L VAL* 2.8 27.7 + - - +
249L ARG* 5.2 2.5 - - + +
260L ILE* 5.3 2.5 - - + -
261L SER 3.8 8.1 - - - +
262L LEU* 4.3 10.5 - - + -
430L ILE* 3.9 24.9 - - + -
431L ALA* 1.3 79.8 - - - +
433L ALA* 1.3 68.1 + - - +
441L LEU* 4.1 30.3 - - + -
444L TYR* 3.8 26.2 - - + -
447L ILE* 3.8 26.9 - - + -
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Residues in contact with ALA 433 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159L VAL* 3.4 29.3 - - + +
162L HIS* 4.2 3.1 - - + -
163L LEU* 3.7 18.2 - - + +
248L VAL* 3.1 23.6 - - + -
250L LEU* 6.0 0.2 - - + -
260L ILE* 3.4 4.3 - - - +
261L SER 3.1 31.2 + - - +
432L ILE* 1.3 81.9 - - - +
434L GLY* 1.3 58.7 + - - +
441L LEU* 5.7 0.7 - - - -
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Residues in contact with GLY 434 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159L VAL* 4.2 5.8 - - - +
248L VAL 3.1 8.9 + - - -
249L ARG* 4.5 1.4 - - - +
250L LEU* 2.7 39.2 + - - +
259L TRP 3.4 10.1 - - - -
260L ILE* 4.4 2.0 - - - -
433L ALA* 1.3 75.6 - - - +
435L THR* 1.3 57.9 + - - -
438L ILE* 3.8 17.7 - - - -
441L LEU* 5.5 3.3 - - - +
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Residues in contact with THR 435 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155L HIS* 4.0 18.8 - - + -
158L ARG* 3.0 26.0 + - - +
159L VAL* 3.3 24.5 - - + -
250L LEU* 2.8 22.3 + - - -
252L ASP* 4.4 1.4 - - - +
255L LEU* 3.9 5.6 - - + +
258L ALA* 3.5 1.4 - - - -
259L TRP* 3.0 45.3 + - + +
434L GLY* 1.3 74.5 - - - -
436L GLY* 1.3 65.2 + - - +
438L ILE* 3.7 4.3 - - - +
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Residues in contact with GLY 436 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251L ARG* 3.6 1.7 - - - +
252L ASP 3.0 40.4 + - - +
255L LEU* 3.6 14.4 - - - +
257L LYS 3.5 10.5 - - - -
259L TRP* 4.3 0.2 - - - -
435L THR* 1.3 80.3 + - - +
437L GLN* 1.3 54.3 + - - -
438L ILE* 2.8 21.5 + - - +
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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