Contacts of the helix formed by residues 311 - 322 (chain F) in PDB entry 5KRA
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 THR 311 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309F SER 4.8 3.8 - - - +
310F LEU* 1.3 78.0 - - - +
312F ALA* 1.3 59.5 + - - +
313F ASP* 3.5 7.5 + - - +
314F GLN* 3.1 40.8 + - - +
315F MET* 3.0 26.6 + - - +
481F LYS* 5.5 1.6 - - - +
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Residues in contact with ALA 312 (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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311F THR* 1.3 74.8 - - - +
313F ASP* 1.3 63.9 + - - +
315F MET* 3.3 4.7 - - - +
316F VAL* 3.1 27.3 + - - +
484F ASP* 5.1 1.1 - - + +
485F THR* 3.7 20.6 - - - +
488F HIS* 3.4 45.3 - - + +
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Residues in contact with ASP 313 (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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311F THR* 3.3 7.1 + - - +
312F ALA* 1.3 75.4 - - - +
314F GLN* 1.3 55.4 + - + +
316F VAL* 3.1 10.2 + - - +
317F SER* 2.8 40.7 + - - +
488F HIS* 3.3 27.6 + - - -
489F LEU* 5.6 2.3 - - - +
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Residues in contact with GLN 314 (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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309F SER 4.2 2.1 - - - +
310F LEU* 3.3 31.3 - - + +
311F THR* 3.1 43.1 + - - +
313F ASP* 1.3 77.9 - - + +
315F MET* 1.3 57.6 + - - +
317F SER* 3.8 6.9 - - - -
318F ALA* 3.0 31.4 + - - +
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Residues in contact with MET 315 (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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307F ALA* 4.2 13.2 - - + +
310F LEU* 4.4 10.9 - - + +
311F THR 3.0 14.0 + - - +
312F ALA 3.3 10.1 - - - +
314F GLN* 1.3 76.9 - - - +
316F VAL* 1.3 63.4 + - - +
318F ALA* 3.7 2.4 - - - +
319F LEU* 3.1 44.9 + - + +
365F PRO* 3.8 31.0 - - + -
447F CYS* 5.3 0.2 - - - -
478F VAL* 5.4 3.4 - - + +
481F LYS* 4.0 27.8 - - + -
482F ILE* 4.5 20.6 - - + -
485F THR* 3.3 24.9 - - + +
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Residues in contact with VAL 316 (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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312F ALA 3.1 16.0 + - - +
313F ASP* 3.1 10.2 + - - +
315F MET* 1.3 77.6 - - - +
317F SER* 1.3 57.4 + - - +
319F LEU* 3.3 7.3 + - - +
320F LEU* 2.8 43.1 + - + +
443F GLU* 3.6 31.4 - - + +
446F VAL* 5.0 2.2 - - + +
447F CYS* 5.1 2.5 - - - -
485F THR* 3.6 19.5 - - + -
488F HIS* 5.9 0.2 - - + -
489F LEU* 3.8 22.9 - - + -
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Residues in contact with SER 317 (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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313F ASP* 2.8 24.0 + - - +
314F GLN* 3.8 8.6 - - - -
316F VAL* 1.3 74.0 - - - +
318F ALA* 1.3 57.7 + - - +
320F LEU* 3.9 7.0 - - - +
321F ASP* 3.0 32.3 + - - +
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Residues in contact with ALA 318 (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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310F LEU* 4.8 6.1 - - + -
314F GLN 3.0 20.1 + - - +
315F MET* 3.7 4.3 - - - +
317F SER* 1.3 78.7 - - - +
319F LEU* 1.3 63.6 + - - +
321F ASP* 3.9 4.8 - - - +
322F ALA* 3.1 24.8 + - - +
363F ARG* 4.9 6.7 + - - +
365F PRO* 4.4 19.3 - - + -
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Residues in contact with LEU 319 (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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315F MET* 3.1 36.6 + - + +
316F VAL* 3.8 3.6 - - - +
318F ALA* 1.3 77.2 - - - +
320F LEU* 1.3 62.7 + - - +
322F ALA* 3.3 13.1 + - + +
323F GLU* 3.4 16.8 + - - +
360F TRP* 4.8 6.7 + - - +
363F ARG 5.1 0.4 - - - +
364F VAL* 4.5 8.7 - - + -
365F PRO* 3.6 26.9 - - + -
446F VAL* 3.7 40.2 - - + +
447F CYS* 4.2 19.5 - - - -
450F SER* 3.2 25.1 - - - +
482F ILE* 5.3 2.2 - - + -
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Residues in contact with LEU 320 (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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316F VAL* 2.8 39.0 + - + +
317F SER* 3.9 6.1 - - - +
319F LEU* 1.3 76.2 - - - +
321F ASP* 1.3 63.0 + - - +
322F ALA 3.1 1.1 + - - -
323F GLU* 3.2 23.3 + - + +
442F GLY* 4.2 13.0 - - - +
443F GLU* 4.3 14.8 - - + +
446F VAL* 3.8 28.5 - - + -
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Residues in contact with ASP 321 (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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317F SER 3.0 19.1 + - - +
318F ALA* 3.9 5.8 - - - +
320F LEU* 1.3 75.8 - - - +
322F ALA* 1.3 58.3 + - - +
323F GLU 3.3 3.2 + - - +
363F ARG* 2.8 32.2 + - - +
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Residues in contact with ALA 322 (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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318F ALA 3.1 17.4 + - - +
319F LEU* 3.7 9.6 - - + +
320F LEU 3.1 1.0 - - - -
321F ASP* 1.3 78.2 - - - +
323F GLU* 1.3 65.8 + - - +
324F PRO* 3.3 1.0 - - - +
360F TRP* 3.0 29.8 - - + +
363F ARG* 3.7 46.7 + - + +
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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