Contacts of the helix formed by residues 295 - 309 (chain A) in PDB entry 3KCZ
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 GLY 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A GLN* 3.6 1.4 - - - +
294A HIS* 1.3 80.2 - - - +
296A ARG* 1.3 65.5 + - - -
297A ALA 3.4 2.5 + - - +
298A LEU 3.4 1.0 + - - -
299A MET* 3.0 29.5 + - - +
320A LEU* 4.9 1.3 - - - +
322A ARG* 5.0 0.4 - - - -
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Residues in contact with ARG 296 (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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295A GLY* 1.3 71.3 - - - -
297A ALA* 1.3 53.6 + - - +
299A MET* 3.5 15.6 + - + +
300A GLU* 2.8 36.9 + - + +
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Residues in contact with ALA 297 (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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288A CYS* 4.1 8.0 - - - -
293A GLN* 4.1 32.3 - - + +
295A GLY 3.4 0.8 - - - -
296A ARG* 1.3 79.3 - - - +
298A LEU* 1.3 57.6 + - - +
300A GLU* 3.2 15.5 + - - +
301A ALA* 2.8 29.6 + - - +
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Residues in contact with LEU 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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285A ILE* 3.9 20.0 - - + -
288A CYS* 4.2 13.2 - - + -
289A ILE* 4.2 11.2 - - + -
293A GLN 3.3 17.4 + - - +
294A HIS* 3.8 19.1 - - - +
295A GLY 3.4 7.9 + - - +
296A ARG 3.4 0.2 - - - -
297A ALA* 1.3 75.6 - - - +
299A MET* 1.3 61.5 + - - +
301A ALA* 3.2 1.1 + - - -
302A CYS* 2.8 36.8 + - - -
320A LEU* 4.0 8.7 - - + -
321A ILE 3.3 19.5 - - - +
322A ARG* 3.2 45.1 - - + +
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Residues in contact with MET 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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295A GLY* 3.0 18.9 + - - +
296A ARG* 3.5 23.3 - - + +
298A LEU* 1.3 75.0 - - - +
300A GLU* 1.3 61.2 + - - +
302A CYS* 3.9 1.8 - - - +
303A ASN* 3.0 25.1 + - - +
320A LEU* 3.3 33.9 - - + +
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Residues in contact with GLU 300 (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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296A ARG* 2.8 24.2 + - + +
297A ALA* 3.2 16.1 + - - +
299A MET* 1.3 72.7 - - - +
301A ALA* 1.3 67.3 + - + +
303A ASN* 3.1 19.0 + - - +
304A GLU* 3.1 26.0 + - + +
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A SER* 4.7 3.3 - - - +
284A LYS* 4.7 9.0 - - + -
285A ILE* 3.8 29.3 - - + +
288A CYS* 4.2 17.5 - - - -
297A ALA 2.8 19.3 + - - +
298A LEU* 3.8 4.7 - - - +
300A GLU* 1.3 76.1 - - + +
302A CYS* 1.3 65.4 + - - +
304A GLU* 3.5 8.1 + - - +
305A PHE* 3.2 16.6 + - - +
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Residues in contact with CYS 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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285A ILE* 4.0 10.3 - - - -
298A LEU* 2.8 31.8 + - - +
299A MET* 3.9 5.8 - - - +
301A ALA* 1.3 74.7 - - - +
303A ASN* 1.3 66.0 + - - +
305A PHE* 3.2 4.6 + - - +
306A TYR* 2.9 43.2 + - + -
318A PRO 6.0 0.2 - - - +
319A PRO 4.6 0.2 - - - +
320A LEU* 3.9 10.5 - - + -
321A ILE* 3.2 49.6 - - + +
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Residues in contact with ASN 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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299A MET 3.0 13.7 + - - +
300A GLU* 3.1 27.2 + - - +
302A CYS* 1.3 76.7 - - - +
304A GLU* 1.3 65.9 + - - +
306A TYR* 3.2 12.4 + - - +
307A THR* 2.9 33.8 + - - -
318A PRO* 6.3 0.4 - - - -
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Residues in contact with GLU 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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281A SER* 2.6 26.9 + - - +
284A LYS* 3.3 34.7 + - - +
300A GLU* 3.1 16.7 + - + +
301A ALA* 3.5 6.9 + - - +
302A CYS 3.3 0.2 - - - -
303A ASN* 1.3 84.6 + - - +
305A PHE* 1.3 66.8 + - - +
307A THR* 3.2 8.7 + - - -
308A ARG* 3.1 41.3 + - + +
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Residues in contact with PHE 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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278A GLY* 3.6 21.1 - - - -
281A SER* 3.7 13.0 - - - -
282A LEU* 3.6 25.8 - - + -
285A ILE* 3.9 11.2 - - + -
301A ALA 3.2 13.9 + - - +
302A CYS 3.2 6.7 + - - +
304A GLU* 1.3 75.1 - - - +
306A TYR* 1.3 67.8 + + - +
308A ARG* 3.0 5.9 + - - +
309A ILE* 2.8 59.5 + - + -
311A HIS* 3.6 17.0 - + - -
321A ILE* 4.1 9.0 - - + -
330A LYS* 3.5 42.2 - - + -
333A LEU* 5.2 1.1 - - + -
334A LEU* 4.4 6.5 - - + -
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Residues in contact with TYR 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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264A LYS* 5.8 1.6 + - - -
302A CYS* 2.9 35.0 + - + -
303A ASN* 3.5 10.8 - - - +
304A GLU 3.2 0.2 - - - -
305A PHE* 1.3 92.4 - + - +
307A THR* 1.3 55.3 + - - +
309A ILE 3.8 3.4 - - - -
310A PRO* 3.2 27.7 - - - +
311A HIS* 3.6 29.2 + + + +
313A PHE* 3.5 30.7 - + + -
318A PRO* 4.0 24.5 - - + -
319A PRO* 2.6 32.4 + - - +
321A ILE* 3.4 19.0 - - + +
330A LYS* 4.9 3.6 + - + +
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Residues in contact with THR 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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264A LYS* 5.9 3.9 - - - +
303A ASN* 2.9 21.2 + - - -
304A GLU* 3.5 12.6 - - + -
305A PHE 3.2 0.2 - - - -
306A TYR* 1.3 78.3 - - - +
308A ARG* 1.3 63.6 + - + +
310A PRO* 4.1 10.6 - - - +
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Residues in contact with ARG 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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274A GLN* 4.9 10.9 - - - +
277A ALA* 3.1 39.0 + - + +
278A GLY* 4.6 7.6 - - - +
280A GLN* 4.2 13.1 + - - +
281A SER* 3.1 25.8 + - - -
284A LYS* 4.7 8.5 - - - +
304A GLU* 3.1 34.4 + - - +
305A PHE 3.0 7.2 + - - +
307A THR* 1.3 81.7 - - + +
309A ILE* 1.3 73.9 + - + +
310A PRO* 3.4 8.2 - - - +
411B GLY* 6.3 0.6 - - - -
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Residues in contact with ILE 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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260A TYR* 3.8 25.6 - - + -
270A LEU* 5.6 2.5 - - + -
274A GLN* 3.8 25.8 - - + +
275A ILE* 4.6 3.1 - - + -
278A GLY* 3.9 8.7 - - - -
305A PHE* 2.8 31.3 + - + +
306A TYR* 3.3 9.1 - - - +
308A ARG* 1.3 84.4 - - - +
310A PRO* 1.4 55.2 - - - +
311A HIS* 2.7 40.4 + - + -
333A LEU* 4.4 3.1 - - + -
334A LEU* 3.7 27.6 - - + -
337A LEU* 4.0 16.2 - - + -
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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