Contacts of the helix formed by residues 302 - 317 (chain A) in PDB entry 1K4S
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 PHE 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A PHE* 4.1 5.6 - + - -
257A ALA* 3.5 42.2 - - + -
260A PHE* 4.2 14.6 - + + -
261A ALA* 3.9 9.4 - - + -
264A LEU* 3.6 28.9 - - + -
278A PHE* 4.1 9.4 - + - -
282A TRP* 3.3 30.7 - + - -
297A LEU* 5.3 5.6 - - + -
300A CYS* 3.6 22.2 - - + -
301A ASP* 1.3 74.4 - - - +
303A THR* 1.3 52.9 + - - +
304A GLN 3.2 2.7 - - - -
305A MET* 2.7 34.1 + - - +
306A SER* 2.7 31.7 + - - -
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Residues in contact with THR 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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264A LEU* 4.0 14.2 - - + +
301A ASP* 2.6 39.1 + - - +
302A PHE* 1.3 76.7 - - - +
304A GLN* 1.3 68.4 + - - +
306A SER* 3.0 6.4 + - - -
307A GLN* 2.9 31.4 + - - +
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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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237A ASN 3.2 15.6 + - - -
238A VAL* 3.4 8.8 - - + +
239A LYS* 2.5 49.4 - - - +
240A PHE 3.2 15.9 - - - +
241A TYR* 3.5 16.8 - - + -
246A VAL* 4.8 0.5 - - - +
301A ASP* 3.9 7.8 + - - +
302A PHE 3.2 0.4 - - - -
303A THR* 1.3 82.4 + - - +
305A MET* 1.3 60.5 + - + +
307A GLN* 2.9 33.7 - - + +
308A TYR* 3.2 6.4 + - - +
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Residues in contact with MET 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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234A LEU* 5.0 15.0 - - + -
238A VAL* 6.1 2.5 - - - -
239A LYS 3.8 17.7 - - - +
240A PHE* 3.5 26.0 - - + -
249A LEU* 5.7 5.6 - - + -
254A GLU* 4.8 1.6 - - - +
257A ALA* 4.1 19.7 - - + -
258A THR* 4.3 19.5 - - + +
261A ALA* 3.7 10.3 - - + -
301A ASP 4.4 3.1 - - - +
302A PHE* 2.7 47.7 + - - +
304A GLN* 1.3 69.7 - - - +
306A SER* 1.3 64.8 + - - +
307A GLN 3.4 0.2 + - - -
308A TYR* 3.4 12.4 + - - +
309A PHE* 3.3 25.7 + - + -
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Residues in contact with SER 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 ALA 3.8 15.0 + - - -
262A LYS* 5.7 0.2 - - - +
264A LEU* 3.4 28.5 - - - +
265A ASP* 5.3 4.3 + - - -
302A PHE 2.7 8.3 + - - -
303A THR* 3.1 11.2 - - - -
305A MET* 1.3 74.4 - - - +
307A GLN* 1.3 69.6 + - - +
309A PHE* 3.1 6.5 + - - +
310A LYS* 3.0 42.8 + - - +
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Residues in contact with GLN 307 (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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303A THR* 2.9 29.7 - - - +
304A GLN* 2.9 17.9 - - + +
306A SER* 1.3 84.9 + - - +
308A TYR* 1.3 48.9 + - - +
310A LYS* 3.1 16.6 + - - +
311A ALA* 2.7 37.7 + - - +
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Residues in contact with TYR 308 (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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234A LEU* 4.9 5.8 - - + -
235A PRO* 3.8 18.9 - - + +
238A VAL* 3.3 52.5 - - + -
304A GLN 3.2 5.9 + - - +
305A MET* 3.7 10.3 - - - +
306A SER 3.3 0.2 - - - -
307A GLN* 1.3 77.3 - - - +
309A PHE* 1.3 71.5 + + + +
311A ALA* 2.7 10.7 + - + +
312A GLN* 2.5 57.9 + - + +
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Residues in contact with PHE 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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231A TYR* 5.9 2.7 - + - -
234A LEU* 4.8 12.6 - - + -
258A THR* 4.1 23.6 - - + -
261A ALA* 5.2 1.1 - - + -
262A LYS* 3.3 56.3 - - + -
305A MET* 3.3 27.1 + - + -
306A SER* 3.1 7.8 + - - +
308A TYR* 1.3 93.3 - + + +
310A LYS* 1.3 51.0 + - + +
312A GLN* 3.1 26.9 + - + +
313A THR* 2.4 43.3 + - - +
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Residues in contact with LYS 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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265A ASP* 5.6 9.9 - - - -
306A SER* 3.0 37.8 + - - +
307A GLN* 3.4 17.0 - - - +
309A PHE* 1.3 75.7 - - + +
311A ALA* 1.3 58.0 + - - +
313A THR* 2.9 10.8 - - - -
314A GLU* 2.8 29.6 + - - +
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Residues in contact with ALA 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 GLN 2.7 18.1 + - - +
308A TYR* 2.7 15.9 + - + +
310A LYS* 1.3 69.1 - - - +
312A GLN* 1.3 54.1 + - - +
313A THR 2.7 4.5 + - - -
314A GLU* 2.8 7.8 + - - +
315A ALA* 2.6 36.4 + - - +
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Residues in contact with GLN 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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308A TYR* 2.5 37.5 + - + +
309A PHE* 3.1 40.5 + - + +
311A ALA* 1.3 72.9 - - - +
313A THR* 1.3 59.5 + - - +
315A ALA* 3.1 9.5 - - - +
316A ARG* 2.6 40.0 + - + +
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Residues in contact with THR 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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309A PHE* 2.4 25.4 + - - +
310A LYS* 2.9 14.8 - - - +
311A ALA 2.7 0.8 + - - -
312A GLN* 1.3 83.7 + - - +
314A GLU* 1.3 55.8 + - - +
315A ALA 2.9 0.7 - - - -
316A ARG* 2.6 12.0 + - + +
317A LYS* 2.5 39.3 + - + +
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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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310A LYS 2.8 14.8 + - - +
311A ALA* 3.6 8.7 - - - +
313A THR* 1.3 74.0 - - - +
315A ALA* 1.3 54.0 + - - +
317A LYS* 2.6 40.8 - - - +
318A GLN* 3.0 6.3 - - - +
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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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311A ALA 2.6 16.8 + - - +
312A GLN* 3.1 17.3 - - - +
314A GLU* 1.3 69.2 - - - +
316A ARG* 1.3 55.7 + - - +
318A GLN* 2.7 31.0 + - - +
319A MET* 2.9 11.9 + - - +
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Residues in contact with ARG 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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312A GLN* 2.6 21.4 + - + +
313A THR* 2.6 18.8 + - + +
315A ALA* 1.3 71.2 - - - +
317A LYS* 1.3 49.6 + - - +
318A GLN 2.8 10.7 + - - -
319A MET* 3.1 22.6 + - - +
324A LYS* 4.5 6.9 - - - +
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Residues in contact with LYS 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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313A THR* 2.5 23.1 + - + +
314A GLU* 2.6 24.2 - - - +
316A ARG* 1.3 68.8 - - - +
318A GLN* 1.3 56.0 + - - +
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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