Contacts of the strand formed by residues 345 - 348 (chain F) in PDB entry 1K9V
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 LEU 345 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302F ARG 3.3 1.4 + - - -
303F ILE* 3.3 30.7 - - + +
304F GLY 2.7 33.3 + - - +
343F TYR* 3.7 3.4 - - - +
344F ASP* 1.3 79.1 - - + +
346F LEU* 1.3 58.8 + - - +
347F PHE* 3.4 37.9 - - + -
379F TYR* 3.3 7.4 - - + +
381F VAL* 3.9 26.5 - - + -
493F VAL* 4.1 11.2 - - + -
494F ILE* 4.2 7.9 - - + -
497F SER* 3.7 28.7 - - - +
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Residues in contact with LEU 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304F GLY* 3.4 22.0 - - - +
306F ILE* 4.0 22.2 - - + -
335F VAL* 4.3 8.7 - - + -
343F TYR* 4.5 6.7 - - + -
344F ASP 4.2 0.2 - - - -
345F LEU* 1.3 75.3 - - - +
347F PHE* 1.3 59.7 + - - +
348F ILE* 4.0 2.6 + - + -
369F PHE* 4.5 7.0 - - + -
370F VAL* 4.2 25.4 - - + -
373F HIS* 3.4 47.6 - - + +
379F TYR 2.8 13.4 + - - +
380F VAL* 3.3 9.3 - - + +
381F VAL 2.7 32.1 + - - +
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Residues in contact with PHE 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303F ILE* 3.8 15.5 - - + -
304F GLY 2.7 20.1 + - - +
305F ILE* 4.2 19.1 - - + -
306F ILE* 3.0 33.4 + - - +
316F LEU* 4.3 12.1 - - + -
320F VAL* 3.9 24.2 - - + -
345F LEU* 3.4 40.2 - - + -
346F LEU* 1.3 73.8 - - - +
348F ILE* 1.3 61.3 + - - +
349F PRO* 3.3 2.5 - - + +
381F VAL* 3.3 23.6 - - + -
383F VAL* 4.0 22.2 - - + -
490F LEU* 4.4 17.3 - - + -
493F VAL* 4.2 11.7 - - + -
494F ILE* 5.5 2.7 - - + -
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Residues in contact with ILE 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306F ILE* 4.0 21.8 - - + -
346F LEU* 4.6 2.9 - - + +
347F PHE* 1.3 76.3 - - - +
349F PRO* 1.3 63.4 - - + +
361F LEU* 4.6 10.8 - - + -
370F VAL* 3.6 24.7 - - + -
380F VAL* 3.6 30.7 - - + -
381F VAL 2.8 10.4 + - - +
382F GLY* 4.3 3.8 - - - -
383F VAL* 2.9 25.0 + - - -
386F GLY* 3.1 23.3 - - - +
389F LEU* 4.4 13.7 - - + -
390F LEU* 4.4 7.4 - - + -
403F LEU* 3.9 15.0 - - + -
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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