Contacts of the helix formed by residues 312 - 322 (chain A) in PDB entry 1KKQ
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 GLY 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A LEU 3.7 16.6 + - - -
309A LEU* 4.7 1.1 - - - -
311A TYR* 1.3 80.7 - - - +
313A VAL* 1.3 62.9 + - - +
314A TYR 3.4 1.3 + - - -
315A GLU* 3.5 1.2 + - - -
316A ALA* 3.2 9.2 + - - +
382A ILE* 3.0 27.7 - - - +
383A ILE* 4.9 6.1 - - - -
388A ARG* 3.6 20.1 - - - -
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Residues in contact with VAL 313 (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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284A VAL* 4.0 27.1 - - + -
287A LEU* 3.6 15.4 - - + +
309A LEU* 3.1 21.8 + - + +
310A LYS 3.1 24.7 - - - +
311A TYR 4.6 0.2 - - - -
312A GLY* 1.3 78.2 - - - +
314A TYR* 1.3 85.4 + - + +
316A ALA* 3.4 3.6 + - - +
317A ILE* 3.1 40.8 + - + +
383A ILE* 6.4 0.2 - - - -
685E LEU* 4.2 15.5 - - + -
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Residues in contact with TYR 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A SER* 5.6 1.8 - - - -
284A VAL* 6.0 1.6 - - + -
311A TYR 4.6 3.3 + - - +
312A GLY 3.4 0.6 - - - -
313A VAL* 1.3 87.3 - - + +
315A GLU* 1.3 67.8 + - - +
317A ILE* 3.3 15.8 + - + +
318A PHE* 3.0 35.8 + + + -
437A VAL* 3.5 25.6 - - + -
440A HIS* 5.6 4.0 - + - -
775A 471 3.3 56.2 + - + +
682E ASN* 3.5 44.4 - - + -
683E MET* 4.5 4.2 - - + +
685E LEU* 4.0 25.2 - - + +
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Residues in contact with GLU 315 (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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311A TYR 3.4 8.2 + - - +
312A GLY 3.5 0.8 + - - -
313A VAL 3.5 0.4 - - - -
314A TYR* 1.3 78.6 - - - +
316A ALA* 1.3 64.2 + - - +
318A PHE* 3.5 2.9 + - - +
319A ALA* 3.1 22.5 + - - +
382A ILE* 3.3 22.3 - - + +
388A ARG* 3.1 41.2 + - - -
430A MET 4.8 4.9 - - - +
433A LEU* 3.7 39.2 - - + +
434A ARG* 3.9 31.5 + - - +
437A VAL* 3.8 13.5 - - + +
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Residues in contact with ALA 316 (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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287A LEU* 3.4 28.7 - - + -
312A GLY 3.2 10.8 + - - +
313A VAL 3.4 9.9 - - - +
314A TYR 3.2 0.2 - - - -
315A GLU* 1.3 79.4 - - - +
317A ILE* 1.3 63.0 + - - +
319A ALA* 3.3 9.2 + - - +
320A MET* 3.1 28.5 + - - +
379A VAL* 4.0 14.3 - - + +
382A ILE* 3.6 12.5 - - + +
383A ILE* 5.1 2.5 - - + -
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Residues in contact with ILE 317 (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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280A SER* 4.8 2.7 - - - +
283A THR* 3.4 34.3 - - + +
284A VAL* 4.8 0.9 - - + -
287A LEU* 4.3 7.0 - - + -
313A VAL* 3.1 34.5 + - + +
314A TYR* 3.6 19.3 - - + +
315A GLU 3.3 0.2 - - - -
316A ALA* 1.3 74.9 - - - +
318A PHE* 1.3 64.1 + - + +
320A MET* 3.1 9.1 + - + +
321A LEU* 2.5 50.5 + - + +
775A 471 4.3 28.5 - - + -
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Residues in contact with PHE 318 (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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314A TYR* 3.0 29.0 + - + +
315A GLU* 4.7 0.4 - - - -
317A ILE* 1.3 77.8 - - + +
319A ALA* 1.3 65.3 + - - +
321A LEU* 3.3 21.3 - - + +
322A SER* 3.0 15.9 + - - -
355A MET* 5.1 1.1 - - + -
358A LYS* 3.4 48.2 - - + -
361A PHE* 4.3 4.3 - - + -
433A LEU* 4.0 17.9 - - + -
436A LEU* 4.6 9.6 - - + -
437A VAL* 3.7 30.3 - - + -
440A HIS* 3.9 22.7 - + - -
775A 471 4.3 26.9 - + + -
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Residues in contact with ALA 319 (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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315A GLU 3.1 14.3 + - - +
316A ALA* 3.3 13.7 - - - +
317A ILE 3.1 0.2 - - - -
318A PHE* 1.3 77.6 - - - +
320A MET* 1.3 60.2 + - - +
322A SER* 3.0 25.0 + - - -
323A SER* 4.3 1.6 + - - -
361A PHE* 4.9 2.9 - - - -
365A PHE* 4.6 10.8 - - + -
375A ILE* 5.3 5.3 - - + +
378A PHE* 4.1 19.7 - - + -
379A VAL* 4.5 8.5 - - + -
382A ILE* 6.1 1.6 - - + -
433A LEU* 3.9 19.7 - - + +
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Residues in contact with MET 320 (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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214A TYR* 3.9 27.1 - - - +
218A PHE* 3.5 38.8 - - + -
220A MET 6.0 2.5 - - - +
287A LEU* 3.7 22.2 - - + -
316A ALA 3.1 17.0 + - - +
317A ILE* 3.1 7.9 + - + +
319A ALA* 1.3 70.9 - - - +
321A LEU* 1.3 55.0 + - - +
322A SER 2.6 6.7 + - - -
323A SER* 2.5 43.8 + - - +
324A VAL* 3.8 3.5 + - - +
375A ILE* 4.4 7.4 - - + -
379A VAL* 4.0 19.5 - - + -
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Residues in contact with LEU 321 (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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317A ILE* 2.5 34.6 + - + +
318A PHE* 3.3 25.8 - - + +
319A ALA 3.2 0.2 - - - -
320A MET* 1.3 72.1 - - - +
322A SER* 1.3 52.0 + - - +
324A VAL* 3.0 20.8 - - + +
325A MET* 2.8 42.6 - - + +
330A MET* 3.5 37.0 - - + -
355A MET* 3.5 23.3 - - + -
358A LYS* 4.8 2.7 - - + -
775A 471 4.2 15.5 - - + +
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Residues in contact with SER 322 (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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318A PHE 3.0 9.9 + - - -
319A ALA 3.0 17.5 + - - -
320A MET 2.6 1.2 + - - -
321A LEU* 1.3 78.0 - - - +
323A SER* 1.3 62.3 + - - +
324A VAL 3.3 0.2 - - - -
325A MET* 3.4 9.4 + - - +
361A PHE* 3.6 13.5 - - - -
362A ALA* 3.5 32.2 - - - +
365A PHE* 4.3 7.6 - - - -
366A ASN* 2.9 37.3 - - - +
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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