Contacts of the helix formed by residues 296 - 309 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264B GLN* 4.6 4.5 + - - -
294B ILE* 3.5 8.1 - - - +
295B LYS* 1.3 82.6 - - - +
297B ALA* 1.3 64.8 + - - +
298B GLU* 2.7 26.9 + - - +
299B GLU* 3.0 22.4 + - - +
300B GLN 3.0 17.8 + - - -
339B PHE* 4.2 8.7 - - - -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B SER* 1.3 73.4 - - - +
298B GLU* 1.3 68.5 + - + +
300B GLN* 3.1 6.2 + - - +
301B ASN* 2.9 38.2 + - - +
339B PHE* 4.6 5.2 - - + -
342B TYR* 3.4 25.8 - - - +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B PHE* 3.8 5.9 - - + -
264B GLN* 4.2 25.1 + - - +
296B SER* 2.7 25.6 + - - +
297B ALA* 1.3 87.9 + - + +
299B GLU* 1.3 56.2 + - - +
301B ASN* 3.2 13.3 + - - +
302B PHE* 2.9 30.1 + - - +
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B PHE* 3.7 18.1 - - + -
264B GLN* 5.4 0.2 - - - +
266B ASN* 5.9 0.7 - - - -
268B TYR* 3.0 27.5 + - + +
292B VAL* 4.6 0.3 - - - +
293B VAL 3.5 3.6 - - - +
294B ILE* 3.9 6.7 - - + -
295B LYS* 2.6 36.6 + - - +
296B SER* 3.0 19.5 + - - +
298B GLU* 1.3 79.9 - - - +
300B GLN* 1.3 57.4 + - - +
302B PHE* 3.4 1.4 + - - +
303B LEU* 2.8 48.2 + - + +
378B LYS* 2.9 29.3 + - - +
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Residues in contact with GLN 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ILE* 3.8 18.3 - - + +
296B SER 3.0 12.1 + - - +
297B ALA* 3.1 11.9 + - - +
299B GLU* 1.3 73.8 - - - +
301B ASN* 1.3 63.7 + - - +
303B LEU* 3.2 3.8 + - - +
304B GLN* 2.7 71.8 + - - +
339B PHE* 5.7 0.2 - - + -
342B TYR* 3.3 45.7 - - + +
359B PHE* 3.8 2.9 - - - -
362B ASN 4.7 2.2 + - - -
364B TRP* 2.8 31.9 + - + +
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Residues in contact with ASN 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B ALA* 2.9 27.6 + - - +
298B GLU* 3.6 15.3 - - - +
300B GLN* 1.3 81.7 + - - +
302B PHE* 1.3 64.3 + - - +
304B GLN* 3.8 5.4 - - - +
305B LEU* 3.0 25.1 + - - +
342B TYR* 4.9 6.2 + - - -
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Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B THR* 4.2 21.1 - - + -
262B PHE 5.0 0.7 - - - -
263B PHE* 3.7 58.1 - + + -
268B TYR* 4.0 20.4 - + + -
270B MET* 5.6 0.9 - - + -
298B GLU 2.9 17.0 + - - +
299B GLU 3.6 2.0 - - - +
301B ASN* 1.3 76.7 - - - +
303B LEU* 1.3 83.1 + - + +
305B LEU* 3.3 11.9 + - + +
306B GLN* 3.2 55.9 + - + +
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Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B TYR* 3.7 29.6 - - + -
270B MET* 5.8 0.2 - - - -
292B VAL* 3.5 20.2 - - + -
294B ILE* 3.5 33.7 - - + -
299B GLU* 2.8 36.7 + - + +
300B GLN 3.7 2.2 - - - +
302B PHE* 1.3 79.7 - - + +
304B GLN* 1.3 62.1 + - - +
306B GLN* 2.8 28.9 + - + +
307B SER* 3.4 9.9 + - - -
359B PHE* 3.7 17.5 - - + -
376B ILE* 4.3 19.3 - - + +
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Residues in contact with GLN 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B GLN* 2.7 43.0 + - - +
301B ASN* 3.8 5.4 - - - +
303B LEU* 1.3 73.8 - - - +
305B LEU* 1.3 57.6 + - - +
307B SER* 3.2 5.9 + - - -
308B SER* 3.0 27.6 + - - -
359B PHE* 3.3 31.2 - - - +
360B SER 4.1 1.0 - - - +
361B GLY 3.1 23.0 + - - +
362B ASN* 3.2 23.3 - - - +
363B GLY* 3.3 28.0 + - - +
364B TRP* 3.6 1.9 - - - -
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ASN 3.0 17.0 + - - +
302B PHE* 3.5 9.9 - - + +
303B LEU 3.0 0.6 - - - -
304B GLN* 1.3 75.3 - - - +
306B GLN* 1.3 62.3 + - - +
307B SER 3.1 6.2 + - - -
308B SER* 3.9 10.1 - - - +
309B ARG* 3.0 66.3 + - + +
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Residues in contact with GLN 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ASN* 4.9 2.3 + - - -
261B THR* 5.2 2.5 + - - +
270B MET* 3.6 42.8 - - + +
302B PHE* 3.2 54.6 + - + +
303B LEU* 2.8 14.6 + - + +
305B LEU* 1.3 83.0 - - - +
307B SER* 1.3 57.7 + - - +
309B ARG* 4.1 29.1 + - - +
310B SER* 3.5 16.3 + - - -
376B ILE* 4.9 4.0 - - + -
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Residues in contact with SER 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LEU 3.4 7.5 + - - -
304B GLN* 3.2 9.6 + - - -
305B LEU 3.1 0.4 - - - -
306B GLN* 1.3 79.6 - - - +
308B SER* 1.3 59.5 + - - +
309B ARG 3.3 1.8 - - - -
310B SER* 3.4 3.8 + - - -
311B ASN* 2.8 25.1 + - - -
312B ARG* 3.2 25.3 + - - +
314B THR* 3.8 11.7 + - - -
359B PHE* 3.4 33.3 - - - +
361B GLY 5.4 1.3 - - - -
376B ILE* 4.5 5.0 - - - +
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Residues in contact with SER 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLN* 3.0 17.6 + - - -
305B LEU* 3.8 12.8 + - - -
307B SER* 1.3 76.5 - - - +
309B ARG* 1.3 63.0 + - - +
311B ASN* 3.2 24.2 + - - +
361B GLY* 3.7 21.5 + - - +
362B ASN* 4.2 11.0 + - - -
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Residues in contact with ARG 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 3.0 57.7 + - + +
306B GLN* 4.1 23.9 + - - +
307B SER 3.3 0.6 - - - -
308B SER* 1.3 78.2 - - - +
310B SER* 1.3 58.2 + - - +
311B ASN* 5.2 3.2 + - - -
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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