Contacts of the helix formed by residues 296 - 310 (chain C) in PDB entry 1K9I
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 SER 296 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264C GLN* 4.5 6.8 + - - -
294C ILE* 3.5 6.4 - - - +
295C LYS* 1.3 81.3 - - - +
297C ALA* 1.3 66.0 + - - +
298C GLU* 3.3 19.6 + - - +
299C GLU* 3.1 33.8 + - - +
300C GLN* 3.1 10.0 + - - +
339C PHE* 4.2 6.5 - - - -
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Residues in contact with ALA 297 (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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296C SER* 1.3 73.7 - - - +
298C GLU* 1.3 77.0 + - - +
300C GLN* 3.1 6.4 + - - +
301C ASN* 3.0 32.6 + - - +
339C PHE* 4.6 5.0 - - + -
342C TYR* 3.5 24.0 - - - +
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Residues in contact with GLU 298 (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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263C PHE* 3.8 6.4 - - + -
264C GLN* 4.2 24.0 - - - +
296C SER* 3.3 22.0 - - - +
297C ALA* 1.3 93.9 + - - +
299C GLU* 1.3 60.9 + - - +
301C ASN* 3.5 13.8 + - - +
302C PHE* 3.1 21.8 + - - +
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Residues in contact with GLU 299 (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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263C PHE* 4.0 17.0 - - + -
266C ASN* 5.8 0.4 - - - -
268C TYR* 2.5 35.6 + - + +
292C VAL* 4.3 0.2 - - - +
293C VAL 3.6 1.7 - - - +
294C ILE* 4.0 7.4 - - + -
295C LYS* 2.8 32.9 + - - +
296C SER* 3.1 21.0 + - - +
298C GLU* 1.3 73.8 - - - +
300C GLN* 1.3 62.5 + - - +
302C PHE* 3.2 1.8 + - + +
303C LEU* 2.8 49.2 + - + +
378C LYS* 2.7 25.2 + - - +
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Residues in contact with GLN 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ILE* 3.5 20.6 - - + +
296C SER 3.1 10.4 + - - +
297C ALA 3.4 8.3 - - - +
299C GLU* 1.3 77.7 - - - +
301C ASN* 1.3 60.9 + - - +
303C LEU* 4.6 0.9 - - - -
304C GLN* 2.8 67.2 + - - +
342C TYR* 3.6 49.7 - - + +
359C PHE* 3.7 2.9 - - - -
362C ASN 4.7 3.2 + - - -
363C GLY* 5.0 0.4 - - - -
364C TRP* 2.8 31.0 + - - +
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Residues in contact with ASN 301 (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 ALA* 3.0 25.7 + - - +
298C GLU* 3.7 12.7 + - - +
300C GLN* 1.3 82.7 + - - +
302C PHE* 1.3 63.7 + - - +
304C GLN* 4.0 3.8 - - - +
305C LEU* 3.2 33.7 + - + +
342C TYR* 4.9 6.8 + - - -
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Residues in contact with PHE 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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261C THR* 4.0 19.1 - - + -
263C PHE* 3.7 35.0 - + + -
268C TYR* 3.7 28.9 - + + -
270C MET* 5.5 2.9 - - - -
298C GLU 3.1 12.0 + - - +
299C GLU* 3.2 6.3 + - + +
301C ASN* 1.3 80.0 - - - +
303C LEU* 1.3 93.2 + - + +
305C LEU* 3.7 2.1 - - - +
306C GLN* 3.1 55.2 + - + +
337H PRO* 4.1 10.9 - - - +
338H SER* 3.9 33.4 - - - -
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Residues in contact with LEU 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C TYR* 3.8 16.8 - - + -
270C MET* 5.8 2.0 - - - -
292C VAL* 3.6 26.5 - - + -
294C ILE* 3.6 24.9 - - + -
299C GLU* 2.8 34.1 + - + +
300C GLN 3.9 1.6 - - - +
302C PHE* 1.3 99.1 - - + +
304C GLN* 1.3 61.2 + - - +
306C GLN* 3.3 6.5 + - + +
307C SER* 2.9 29.5 + - - -
359C PHE* 3.9 16.8 - - + -
376C ILE* 4.5 18.9 - - + +
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Residues in contact with GLN 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 GLN* 2.8 44.1 + - - +
301C ASN* 4.0 4.0 - - - +
303C LEU* 1.3 72.7 - - - +
305C LEU* 1.3 58.6 + - + +
307C SER* 3.4 3.4 + - - -
308C SER* 2.9 28.9 + - - -
359C PHE* 3.3 25.5 - - - +
360C SER 3.9 7.3 - - - +
361C GLY 2.8 26.0 + - - +
362C ASN* 3.4 22.9 - - - +
363C GLY* 3.1 30.0 + - - +
364C TRP* 3.4 1.2 - - - -
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Residues in contact with LEU 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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301C ASN* 3.2 21.2 + - + +
302C PHE 3.7 1.1 - - - +
304C GLN* 1.3 78.0 - - + +
306C GLN* 1.3 60.0 + - - +
308C SER* 3.6 9.2 - - - -
309C ARG* 2.8 50.1 + - + +
337H PRO* 3.7 21.5 - - + -
340H LYS* 3.7 26.9 - - + +
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Residues in contact with GLN 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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261C THR* 4.5 4.9 + - - +
270C MET* 4.1 34.2 - - + +
302C PHE* 3.1 42.7 + - + +
303C LEU* 3.3 8.7 + - + +
305C LEU* 1.3 75.3 - - - +
307C SER* 1.3 62.9 + - - +
309C ARG* 3.5 9.7 + - - +
310C SER* 3.1 24.3 + - - -
376C ILE* 6.0 2.2 - - + -
336H LEU* 5.0 5.1 - - - +
337H PRO* 3.6 30.7 - - + +
338H SER* 4.2 8.4 + - - +
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Residues in contact with SER 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C LEU 2.9 14.7 + - - -
304C GLN* 3.6 8.1 - - - -
306C GLN* 1.3 77.7 - - - +
308C SER* 1.3 62.1 + - - +
310C SER* 2.7 23.5 + - - -
311C ASN 3.2 5.9 + - - -
312C ARG 3.5 12.9 + - - +
314C THR* 4.2 13.0 + - - -
359C PHE* 3.7 35.8 - - - +
376C ILE* 4.0 12.2 - - - +
5L NAG 4.3 2.4 + - - -
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Residues in contact with SER 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C GLN 2.9 18.6 + - - -
305C LEU* 3.3 14.3 + - - -
307C SER* 1.3 76.5 - - - +
309C ARG* 1.3 62.5 + - - +
311C ASN* 3.0 14.2 + - - +
361C GLY* 3.4 24.3 + - - -
5L NAG 3.3 30.0 + - - -
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Residues in contact with ARG 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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305C LEU* 2.8 41.6 + - + +
306C GLN* 3.7 9.9 - - - +
307C SER 3.3 0.2 - - - -
308C SER* 1.3 72.6 - - - +
310C SER* 1.3 58.2 + - - +
311C ASN* 3.2 17.7 + - - -
334H PRO* 4.5 24.8 - - - +
335H LEU 5.5 2.9 + - - -
336H LEU* 4.5 16.5 - - - +
337H PRO* 3.7 34.4 - - - +
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Residues in contact with SER 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C MET* 6.2 1.3 - - - +
306C GLN 3.1 15.1 + - - -
307C SER* 2.7 22.0 + - - -
309C ARG* 1.3 74.5 - - - +
311C ASN* 1.3 71.5 + - - +
312C ARG* 3.2 26.2 + - - +
314C THR* 5.1 1.0 + - - -
272F ASN* 5.6 1.1 - - - -
312F ARG* 3.8 26.2 + - - +
374F PHE* 6.3 2.2 - - - -
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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