Contacts of the helix formed by residues 308 - 322 (chain A) in PDB entry 1KAS
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 PRO 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A ARG* 3.5 46.7 + - + +
227A ASP* 4.8 2.7 - - - -
228A GLY* 4.3 11.4 - - - +
306A SER 4.1 4.7 - - - +
307A THR* 1.3 90.5 - - + +
309A ALA* 1.3 63.0 + - - +
312A LYS* 3.5 20.5 + - - +
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Residues in contact with ALA 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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271A SER* 5.2 7.0 - - - +
272A PRO* 4.3 19.9 - - + +
274A GLU* 5.4 13.9 - - + +
307A THR* 3.4 2.3 - - - -
308A PRO* 1.3 81.2 - - - +
310A GLY* 1.3 61.8 + - - +
312A LYS* 3.6 6.8 + - - +
313A ALA* 3.3 21.7 + - - +
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Residues in contact with GLY 310 (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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272A PRO* 3.9 19.1 - - - +
303A HIS* 6.6 0.2 - - - -
305A THR* 5.3 1.3 - - - -
307A THR* 3.4 18.9 + - - -
309A ALA* 1.3 77.9 - - - +
311A ASP* 1.3 64.0 + - - +
313A ALA* 3.4 2.6 + - - +
314A GLU* 3.2 24.3 + - - +
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Residues in contact with ASP 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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221A PRO* 3.2 4.6 - - - +
222A TRP* 2.9 56.7 + - + +
226A ARG* 3.0 32.5 - - - +
304A GLY* 3.9 4.0 - - - -
305A THR 3.4 11.1 + - - -
306A SER* 3.1 28.5 + - - -
307A THR* 2.9 15.8 + - - +
310A GLY* 1.3 76.8 - - - +
312A LYS* 1.3 60.5 + - - +
314A GLU* 3.7 4.1 + - - +
315A ALA* 3.2 11.8 + - - +
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Residues in contact with LYS 312 (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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222A TRP* 5.3 0.7 - - - -
226A ARG* 4.4 6.1 - - - +
274A GLU* 3.9 27.3 + - - +
308A PRO 3.5 15.9 + - - +
309A ALA* 3.9 8.5 - - - +
310A GLY 3.3 0.4 - - - -
311A ASP* 1.3 77.2 - - - +
313A ALA* 1.3 64.1 + - - +
315A ALA* 3.4 6.8 + - - +
316A GLN* 3.0 24.8 + - - +
372A ASP* 3.6 26.5 - - + +
374A GLY* 5.8 7.2 - - - +
375A CYS* 5.7 4.0 - - - -
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Residues in contact with ALA 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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272A PRO* 4.3 14.4 - - + -
273A PRO 3.3 25.6 - - - +
274A GLU* 3.7 13.4 + - - +
276A GLY* 3.6 11.1 - - - -
279A ALA* 5.7 0.7 - - + -
309A ALA 3.3 16.0 + - - +
310A GLY 3.4 4.7 + - - +
312A LYS* 1.3 78.2 - - - +
314A GLU* 1.3 58.1 + - - +
316A GLN* 3.2 5.2 + - - +
317A ALA* 2.9 28.4 + - - +
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Residues in contact with GLU 314 (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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222A TRP* 4.2 7.1 - - + -
279A ALA* 5.1 1.6 - - - -
300A VAL* 5.1 1.0 - - - +
302A ALA* 3.1 19.0 - - + +
303A HIS* 2.8 23.7 + - - +
304A GLY* 2.8 31.2 + - - -
310A GLY 3.2 13.6 + - - +
311A ASP* 4.0 4.6 - - - +
313A ALA* 1.3 73.5 - - - +
315A ALA* 1.3 69.5 + - - +
317A ALA* 2.9 18.1 + - + +
318A VAL* 3.0 22.3 + - + +
331A VAL* 5.9 0.4 - - + -
396A ASN* 3.7 8.5 + - - +
398A PHE* 3.6 29.8 - - + -
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Residues in contact with ALA 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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222A TRP* 3.9 16.5 - - + +
311A ASP 3.2 13.9 + - - +
312A LYS* 3.4 12.1 - - - +
313A ALA 3.3 0.2 - - - -
314A GLU* 1.3 80.5 - - - +
316A GLN* 1.3 61.6 + - - +
318A VAL* 3.0 13.3 + - - +
319A LYS* 3.2 18.5 + - + +
374A GLY 5.0 7.0 - - - +
375A CYS* 4.8 9.4 - - - -
377A LEU* 4.0 20.8 - - + +
379A PHE* 4.7 3.6 - - + -
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Residues in contact with GLN 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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274A GLU 4.1 8.0 - - - +
275A ASN* 3.2 26.2 - - - +
312A LYS 3.0 14.3 + - - +
313A ALA 3.4 9.2 - - - +
315A ALA* 1.3 74.3 - - - +
317A ALA* 1.3 59.7 + - - +
319A LYS* 3.5 22.0 + - - +
320A THR* 2.8 34.1 + - - +
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Residues in contact with ALA 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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275A ASN 4.3 2.2 + - - -
276A GLY 3.4 25.4 - - - +
279A ALA* 3.7 18.8 - - + -
280A ALA* 3.8 4.5 - - - +
283A MET* 3.6 10.2 - - + +
313A ALA 2.9 11.9 + - - +
314A GLU 2.9 8.9 + - - +
316A GLN* 1.3 73.7 - - - +
318A VAL* 1.3 61.0 + - - +
320A THR* 3.7 7.2 + - - -
321A ILE* 3.2 30.8 + - - +
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Residues in contact with VAL 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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283A MET* 4.1 19.3 - - + -
300A VAL* 5.2 5.8 - - + -
314A GLU* 3.0 27.0 + - + +
315A ALA* 3.0 7.8 + - - +
317A ALA* 1.3 74.3 - - - +
319A LYS* 1.3 65.6 + - - +
322A PHE* 3.0 49.0 + - + +
329A VAL* 4.5 4.3 - - + -
331A VAL* 4.2 30.7 - - + -
377A LEU* 4.2 19.7 - - + -
396A ASN* 5.2 0.2 - - - +
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Residues in contact with LYS 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 ALA* 3.2 16.4 + - - +
316A GLN* 3.6 28.3 - - - +
318A VAL* 1.3 76.2 - - - +
320A THR* 1.3 57.1 + - - +
323A GLY* 2.9 33.1 + - - +
326A ALA* 4.6 11.2 - - + -
374A GLY* 4.1 19.7 + - - -
375A CYS* 5.6 0.2 - - - +
376A ASP* 3.8 34.7 + - - +
377A LEU* 4.2 20.0 - - + -
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Residues in contact with THR 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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275A ASN* 5.0 6.6 + - - +
280A ALA* 4.7 13.7 - - + -
316A GLN* 2.8 26.5 + - - +
317A ALA* 3.8 9.0 - - - -
318A VAL 3.3 0.2 - - - -
319A LYS* 1.3 77.2 - - - +
321A ILE* 1.3 64.7 + - + +
323A GLY* 4.7 1.9 + - - -
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Residues in contact with ILE 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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280A ALA* 3.3 42.0 - - + +
283A MET* 4.2 13.7 - - + -
284A ALA* 4.2 12.3 - - + -
287A LEU* 3.5 30.5 - - + +
294A ALA* 3.4 10.6 - - + +
317A ALA 3.2 19.3 + - - +
319A LYS 3.3 0.4 - - - -
320A THR* 1.3 83.8 - - + +
322A PHE* 1.3 81.7 + - + +
323A GLY 3.5 0.2 - - - -
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Residues in contact with PHE 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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283A MET* 4.4 6.5 - - - -
287A LEU* 6.1 0.2 - - + -
294A ALA* 3.1 39.4 - - + +
297A ILE* 4.0 14.4 - - + -
300A VAL* 3.6 23.3 - - + -
318A VAL* 3.0 36.5 + - + +
321A ILE* 1.3 93.8 - - + +
323A GLY* 1.3 59.5 + - - +
324A GLU 3.0 9.9 + - - -
325A ALA* 3.2 16.2 + - + +
326A ALA* 3.8 18.6 - - - +
329A VAL* 3.8 29.4 - - + -
394A LEU* 4.1 16.4 - - + -
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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