Contacts of the helix formed by residues 297 - 311 (chain A) 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 ALA 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A SER* 1.3 76.0 - - - +
298A GLU* 1.3 63.6 + - + +
299A GLU 3.4 0.2 - - - -
300A GLN* 3.4 7.8 - - - +
301A ASN* 2.6 40.9 + - - +
342A TYR* 3.5 22.7 + - - +
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Residues in contact with GLU 298 (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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263A PHE* 3.9 17.0 - - + -
264A GLN* 3.0 22.9 + - - +
296A SER* 2.9 23.3 + - - -
297A ALA* 1.3 90.4 + - + +
299A GLU* 1.3 55.0 + - - +
300A GLN 2.9 1.8 - - - -
301A ASN* 2.6 12.1 + - - +
302A PHE* 2.4 36.2 + - - +
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Residues in contact with GLU 299 (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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263A PHE* 3.6 20.3 - - + -
264A GLN* 4.5 2.5 - - - +
268A TYR* 2.8 26.6 + - + +
292A VAL* 4.7 0.5 - - - +
293A VAL 3.2 6.1 - - - +
294A ILE* 3.6 11.6 - - + -
295A LYS* 2.6 40.2 + - - +
296A SER* 2.7 16.6 + - - +
298A GLU* 1.3 75.8 - - - +
300A GLN* 1.3 56.6 + - - +
302A PHE* 3.4 1.4 - - - +
303A LEU* 2.8 45.3 + - + +
378A LYS* 2.7 28.1 + - - -
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Residues in contact with GLN 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ILE* 3.0 43.1 - - + +
297A ALA* 3.4 17.1 + - - +
298A GLU 2.9 0.4 - - - -
299A GLU* 1.3 76.4 - - - +
301A ASN* 1.3 61.1 + - - +
302A PHE 3.2 0.2 + - - -
303A LEU* 3.2 0.6 + - - -
304A GLN* 2.7 80.5 + - - +
342A TYR* 3.8 34.9 - - + +
359A PHE* 3.9 2.6 - - - -
362A ASN 4.8 1.8 + - - -
364A TRP* 3.0 22.3 + - - +
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Residues in contact with ASN 301 (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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297A ALA* 2.6 28.5 + - - +
298A GLU* 2.6 15.4 + - - +
300A GLN* 1.3 80.0 - - - +
302A PHE* 1.3 58.0 + - - +
304A GLN* 4.0 4.4 - - - +
305A LEU* 2.8 39.8 + - + +
342A TYR* 6.4 0.2 - - - -
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Residues in contact with PHE 302 (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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261A THR* 3.7 29.4 - - + -
262A PHE 5.1 0.9 - - - -
263A PHE* 3.7 55.6 - + + -
268A TYR* 3.9 19.5 - + + -
270A MET* 5.1 1.6 - - + -
298A GLU 2.4 29.4 + - - +
299A GLU* 3.4 3.1 - - - +
301A ASN* 1.3 68.1 - - - +
303A LEU* 1.3 77.3 + - + +
305A LEU* 3.1 12.4 + - + +
306A GLN* 2.9 71.0 + - + +
309A ARG* 5.4 0.9 - - - -
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Residues in contact with LEU 303 (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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268A TYR* 4.0 24.0 - - + -
270A MET* 5.8 0.7 - - - -
292A VAL* 3.4 28.0 - - + -
294A ILE* 3.8 23.1 - - + -
299A GLU* 2.8 36.6 + - + +
300A GLN 3.7 1.1 - - - +
302A PHE* 1.3 83.4 - - + +
304A GLN* 1.3 67.0 + - - +
305A LEU 2.9 1.6 - - - -
306A GLN* 2.8 20.0 + - + +
307A SER* 3.1 15.2 + - - -
359A PHE* 3.6 22.0 - - + -
376A ILE* 4.4 20.1 - - + +
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Residues in contact with GLN 304 (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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300A GLN* 2.7 49.5 + - - +
301A ASN* 4.0 5.2 - - - +
303A LEU* 1.3 72.3 - - - +
305A LEU* 1.3 58.6 + - + +
307A SER* 4.2 0.9 - - - -
308A SER* 3.0 31.2 + - - +
359A PHE* 3.4 19.5 - - - +
360A SER 4.1 3.8 - - - +
361A GLY 2.8 26.1 + - - +
362A ASN* 3.0 25.4 - - - +
363A GLY 3.1 17.8 + - - -
364A TRP* 3.4 17.8 - - - -
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Residues in contact with LEU 305 (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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301A ASN* 2.8 29.3 + - + +
302A PHE* 3.1 10.0 + - - +
303A LEU 2.9 0.6 - - - -
304A GLN* 1.3 76.1 - - + +
306A GLN* 1.3 65.7 + - - +
307A SER 2.9 2.4 + - - -
308A SER* 3.0 6.9 + - - -
309A ARG* 2.8 60.7 + - + +
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Residues in contact with GLN 306 (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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261A THR* 4.7 6.2 + - - +
270A MET* 3.2 40.1 - - + +
302A PHE* 2.9 66.4 + - + +
303A LEU* 2.8 13.8 + - + +
305A LEU* 1.3 76.1 - - - +
307A SER* 1.3 59.5 + - - +
309A ARG* 3.3 44.9 + - - +
310A SER* 3.0 21.5 + - - -
376A ILE* 5.2 1.1 - - + -
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Residues in contact with SER 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A MET* 5.8 0.6 - - - +
303A LEU 3.1 11.9 + - - -
304A GLN* 4.2 1.6 - - - -
305A LEU 3.0 0.4 - - - -
306A GLN* 1.3 75.7 - - - +
308A SER* 1.3 66.6 + - - +
309A ARG 3.0 2.2 - - - -
310A SER* 3.0 10.4 + - - -
311A ASN 3.0 19.1 + - - -
312A ARG 3.4 22.6 + - - -
314A THR* 3.6 14.9 + - - -
359A PHE* 3.9 25.4 - - - +
376A ILE* 3.9 13.0 - - - +
5K NAG 3.9 3.9 + - - -
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Residues in contact with SER 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLN* 3.0 22.3 + - - -
305A LEU* 3.7 10.3 - - - -
307A SER* 1.3 77.7 - - - +
309A ARG* 1.3 63.1 + - - +
311A ASN* 3.5 5.0 + - - +
361A GLY* 3.8 17.3 + - - -
362A ASN* 4.3 9.4 + - - -
5K NAG 3.5 32.7 + - - -
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Residues in contact with ARG 309 (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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302A PHE* 5.4 0.8 - - - -
305A LEU* 2.8 53.8 + - + +
306A GLN* 3.3 38.9 + - - +
308A SER* 1.3 75.5 - - - +
310A SER* 1.3 57.0 + - - +
311A ASN* 2.8 27.9 + - - -
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Residues in contact with SER 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A MET* 5.6 4.6 - - - +
306A GLN 3.0 16.0 + - - -
307A SER* 3.0 14.7 + - - -
309A ARG* 1.3 78.5 - - - +
311A ASN* 1.3 69.5 + - - +
312A ARG* 3.0 27.2 + - - +
314A THR* 5.3 0.5 + - - -
272B ASN* 5.7 2.7 - - - -
312B ARG* 3.6 26.5 + - - +
374B PHE* 6.2 2.0 - - - -
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Residues in contact with ASN 311 (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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307A SER 3.0 3.8 + - - -
308A SER 3.5 2.6 + - - +
309A ARG 2.8 26.7 + - - -
310A SER* 1.3 77.7 - - - +
312A ARG* 1.3 60.7 + - - +
313A PHE* 4.5 2.8 + - - -
5K NAG 2.8 40.3 + - - +
5N NAG 6.0 4.2 - - - +
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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