Contacts of the helix formed by residues 301 - 312 (chain C) 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 ASP 301 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299C ASN 3.4 1.8 + - - -
300C LEU* 1.3 72.9 - - - +
302C LEU* 1.3 59.1 + - - +
303C ASN* 2.5 26.3 + - - +
304C ASP* 2.5 35.5 + - - +
305C GLN 3.1 4.7 + - - -
392C LEU* 4.6 15.1 - - + +
393C ASN* 3.6 25.9 - - - +
697F TYR* 5.2 7.6 - - + -
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Residues in contact with LEU 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C LEU 3.0 6.7 + - - +
301C ASP* 1.3 76.4 + - - +
303C ASN* 1.3 66.3 + - - +
305C GLN* 3.4 33.5 - - - +
306C VAL* 3.5 13.3 + - + +
695F GLY* 5.0 13.9 - - - +
690G ARG* 5.7 9.6 - - + +
693G LEU* 5.0 13.2 - - + +
694G MET* 4.7 21.1 - - - -
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Residues in contact with ASN 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A GLY* 6.0 1.4 - - - -
301C ASP* 2.5 21.5 + - - +
302C LEU* 1.3 81.3 - - - +
304C ASP* 1.3 63.9 + - - +
305C GLN 3.0 2.5 + - - -
306C VAL* 3.4 6.7 + - - +
307C THR* 2.8 27.8 + - - +
690G ARG* 3.0 31.4 + - - +
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Residues in contact with ASP 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C LEU* 4.1 8.7 - - + -
301C ASP* 2.5 27.2 + - - +
303C ASN* 1.3 73.9 - - - +
305C GLN* 1.3 62.6 + - - +
307C THR* 3.5 5.0 + - - -
308C LEU* 3.1 26.2 + - - +
390C GLY 4.1 2.3 - - - +
391C LEU* 3.2 20.4 - - + +
392C LEU* 2.8 31.4 + - - +
393C ASN* 2.6 40.4 + - - +
397C ILE* 4.1 9.2 - - + -
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Residues in contact with GLN 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C LYS* 4.9 2.8 - - - +
297C PHE* 2.6 55.2 + - + +
298C ALA* 3.6 14.5 + - - +
300C LEU* 3.5 30.9 + - + -
301C ASP 3.1 4.8 + - - +
302C LEU* 3.4 21.6 - - - +
303C ASN 3.0 0.2 - - - -
304C ASP* 1.3 73.2 - - - +
306C VAL* 1.3 54.5 + - - +
307C THR 2.7 5.0 + - - -
308C LEU* 2.6 29.9 + - - +
309C LEU* 3.0 11.8 + - - +
693G LEU* 3.6 28.2 - - + +
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Residues in contact with VAL 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C LEU* 3.5 15.2 + - + +
303C ASN* 3.4 8.5 + - - +
305C GLN* 1.3 78.5 - - - +
307C THR* 1.3 61.3 + - - +
310C LYS* 3.2 27.3 + - + +
686G GLU* 3.6 32.8 - - + +
689G ILE* 3.5 16.1 - - + +
690G ARG* 3.9 40.6 - - + +
693G LEU* 3.8 20.6 - - + +
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Residues in contact with THR 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303C ASN* 2.8 16.9 + - - -
304C ASP* 3.6 8.5 - - - -
305C GLN 2.7 5.1 + - - -
306C VAL* 1.3 74.3 - - - +
308C LEU* 1.3 63.6 + - - -
310C LYS* 3.4 11.0 + - - +
311C TYR* 3.2 45.0 + - + -
388C ARG* 4.8 1.1 - - + -
389C PRO 3.6 24.5 - - - +
390C GLY 4.2 11.2 + - - +
391C LEU* 4.1 17.5 - - + -
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Residues in contact with LEU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C PHE* 4.0 21.1 - - + -
300C LEU* 3.7 30.1 - - + -
304C ASP 3.1 16.9 + - - +
305C GLN 2.6 12.3 + - - +
307C THR* 1.3 73.7 - - - +
309C LEU* 1.3 59.8 + - - +
311C TYR* 4.3 0.9 - - - +
312C GLY* 3.4 20.1 + - - -
383C ILE* 3.8 25.6 - - + +
384C CYS* 4.4 10.5 - - + -
385C CYS 3.7 23.3 - - - +
388C ARG* 3.9 8.5 + - + -
391C LEU* 3.7 18.4 - - + -
397C ILE* 3.7 19.1 - - + -
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Residues in contact with LEU 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C VAL* 5.8 0.2 - - - +
287C LEU* 3.7 21.5 - - + +
288C THR* 3.2 46.2 - - + +
291C ALA* 4.2 7.6 - - + -
297C PHE* 4.1 20.0 - - + -
305C GLN 3.0 9.3 + - - +
308C LEU* 1.3 77.2 - - - +
310C LYS* 1.3 58.5 + - - +
312C GLY 5.4 0.2 - - - -
313C VAL* 2.9 35.6 - - + +
383C ILE* 3.7 29.4 - - + -
689G ILE* 3.7 23.7 - - + +
693G LEU* 4.8 4.0 - - + -
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Residues in contact with LYS 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C VAL* 3.2 25.3 + - + +
307C THR* 3.9 13.7 - - - +
308C LEU 3.3 0.2 - - - -
309C LEU* 1.3 77.0 - - - +
311C TYR* 1.3 99.2 + - + +
313C VAL* 3.9 12.5 - - - +
314C TYR* 5.1 0.2 - - - -
682G ASN 3.9 11.8 + - - +
683G MET 4.3 15.3 + - - +
684G GLY* 4.8 7.7 - - - -
685G LEU* 4.3 15.1 - - + +
686G GLU* 4.5 33.1 + - + +
689G ILE* 4.4 8.7 - - + -
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Residues in contact with TYR 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307C THR* 3.2 35.2 + - + +
310C LYS* 1.3 105.1 + - + +
312C GLY* 1.3 58.8 + - - +
313C VAL* 3.2 6.9 + - - +
314C TYR* 4.2 6.6 + - - +
315C GLU* 4.6 6.4 - - - +
388C ARG* 3.6 29.6 + - + +
389C PRO* 3.3 52.7 + - + +
437C VAL* 5.5 2.4 - - - +
682G ASN* 4.1 26.1 + - - +
683G MET 6.0 0.2 - - - -
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Residues in contact with GLY 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C LEU 3.4 13.4 + - - -
309C LEU 4.6 0.4 - - - -
311C TYR* 1.3 78.3 - - - +
313C VAL* 1.3 58.0 + - - +
314C TYR 3.5 0.9 - - - -
315C GLU* 4.0 10.3 - - - -
316C ALA* 3.9 1.4 - - - +
382C ILE* 3.0 24.3 - - - +
383C ILE* 3.7 12.3 - - - +
388C ARG* 3.2 26.5 - - - +
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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