Contacts of the helix formed by residues 295 - 309 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293B GLN* 3.9 2.6 - - - +
294B HIS* 1.3 80.4 - - - +
296B ARG* 1.3 66.6 + - - -
297B ALA 3.3 2.7 - - - -
298B LEU* 3.2 4.3 + - - +
299B MET* 3.1 23.2 + - - +
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Residues in contact with ARG 296 (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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295B GLY* 1.3 71.4 - - - -
297B ALA* 1.3 56.6 + - - +
299B MET* 3.4 16.8 + - + +
300B GLU* 2.8 62.3 + - + +
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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
----------------------------------------------------------
288B CYS* 3.7 17.5 - - - -
293B GLN* 4.9 10.5 - - + -
295B GLY 3.3 1.0 + - - -
296B ARG* 1.3 79.6 - - - +
298B LEU* 1.3 57.4 + - - +
300B GLU* 3.7 8.3 - - - +
301B ALA* 2.9 28.6 + - - +
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Residues in contact with LEU 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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285B ILE* 4.1 12.8 - - + +
288B CYS* 3.6 28.6 - - + -
289B ILE* 5.2 3.8 - - + -
293B GLN* 3.7 22.4 - - - +
294B HIS* 3.9 28.7 - - + +
295B GLY 3.2 8.3 + - - +
297B ALA* 1.3 75.9 - - - +
299B MET* 1.3 56.4 + - - +
301B ALA* 3.1 2.4 + - - +
302B CYS* 2.7 53.4 + - - +
320B LEU* 4.4 19.1 - - + -
321B ILE 4.1 16.2 - - - +
322B ARG* 4.9 2.9 - - + -
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Residues in contact with MET 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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295B GLY 3.1 13.2 + - - +
296B ARG* 3.7 21.3 - - + +
298B LEU* 1.3 76.6 - - - +
300B GLU* 1.3 85.5 + - + +
302B CYS* 3.3 0.9 + - - +
303B ASN* 2.8 54.7 + - - +
320B LEU* 4.4 15.2 - - + +
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Residues in contact with GLU 300 (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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284B LYS* 5.8 5.1 + - - +
296B ARG* 2.8 56.3 + - + +
297B ALA* 3.7 7.0 - - - +
299B MET* 1.3 97.6 - - + +
301B ALA* 1.3 54.6 + - - +
303B ASN* 3.8 6.0 - - - +
304B GLU* 3.0 29.1 + - - +
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Residues in contact with ALA 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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281B SER* 4.5 3.1 - - - -
284B LYS* 4.1 21.5 - - + +
285B ILE* 3.8 33.5 - - + +
288B CYS* 4.4 1.3 - - - -
297B ALA 2.9 17.6 + - - +
298B LEU* 3.1 9.4 + - - +
300B GLU* 1.3 74.7 - - - +
302B CYS* 1.3 59.2 + - - +
304B GLU* 3.3 7.0 + - - +
305B PHE* 3.0 27.5 + - - +
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Residues in contact with CYS 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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285B ILE* 3.8 21.8 - - + -
298B LEU* 2.7 38.5 + - - +
299B MET 4.0 2.9 - - - +
301B ALA* 1.3 72.2 - - - +
303B ASN* 1.3 58.6 + - - +
305B PHE* 3.3 3.2 + - - +
306B TYR* 3.0 48.7 + - + -
320B LEU* 4.0 16.8 - - + -
321B ILE* 3.5 31.2 - - - -
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Residues in contact with ASN 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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299B MET* 2.8 46.0 + - - +
300B GLU* 3.8 5.5 - - - +
302B CYS* 1.3 75.9 - - - +
304B GLU* 1.3 56.3 + - - +
306B TYR* 3.4 9.7 + - - +
307B THR* 2.7 40.5 + - - +
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Residues in contact with GLU 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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280B GLN 4.9 0.2 - - - -
281B SER* 2.6 27.0 + - - +
284B LYS* 3.2 37.6 + - - +
300B GLU 3.0 17.6 + - - +
301B ALA* 3.3 5.6 + - - +
303B ASN* 1.3 76.8 - - - +
305B PHE* 1.3 63.0 + - - +
307B THR* 3.3 6.8 + - - -
308B ARG* 3.0 55.0 + - + +
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Residues in contact with PHE 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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278B GLY* 3.6 19.5 - - - -
281B SER* 3.8 12.3 - - - -
282B LEU* 3.6 28.9 - - + -
285B ILE* 4.1 9.4 - - + -
301B ALA 3.0 14.1 + - - +
302B CYS 3.3 5.8 + - - +
304B GLU* 1.3 76.8 - - - +
306B TYR* 1.3 64.9 + + - +
308B ARG* 3.2 3.0 + - - +
309B ILE* 2.8 64.1 + - + +
311B HIS* 3.6 26.9 - + - -
321B ILE* 4.0 11.9 - - + -
330B LYS* 3.7 26.2 - - + -
333B LEU* 5.2 1.6 - - + -
334B LEU* 4.3 9.0 - - + -
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Residues in contact with TYR 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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302B CYS* 3.0 34.9 + - + +
303B ASN* 4.0 9.2 - - - +
305B PHE* 1.3 86.3 - + - +
307B THR* 1.3 64.5 + - - +
309B ILE 3.8 3.4 - - - -
310B PRO* 3.3 22.9 - - - +
311B HIS* 3.7 37.6 + + + +
313B PHE* 3.7 27.1 - + - -
318B PRO* 4.0 21.5 - - + -
319B PRO* 2.6 31.7 + - - +
321B ILE* 3.8 17.8 - - + +
330B LYS* 5.2 2.4 + - + +
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Residues in contact with THR 307 (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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303B ASN* 2.7 24.2 + - - +
304B GLU* 3.6 7.7 - - - -
306B TYR* 1.3 81.2 - - - +
308B ARG* 1.3 65.1 + - + +
310B PRO* 4.1 10.6 - - - +
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Residues in contact with ARG 308 (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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417A ARG* 4.1 25.7 - - - +
270B LEU* 5.4 2.9 - - - +
274B GLN* 4.9 11.0 - - - +
277B ALA* 3.0 43.0 + - + +
278B GLY* 4.8 5.4 - - - +
280B GLN* 4.5 7.9 + - - +
281B SER* 3.1 23.4 + - - +
304B GLU* 3.0 44.0 + - + +
305B PHE* 3.8 3.8 - - - +
307B THR* 1.3 83.1 - - + +
309B ILE* 1.3 72.8 + - + +
310B PRO* 3.5 7.6 - - - +
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Residues in contact with ILE 309 (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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260B TYR* 3.9 23.3 - - + -
270B LEU* 5.0 7.9 - - + -
274B GLN 3.9 20.6 - - - +
275B ILE* 4.5 5.4 - - - -
278B GLY* 3.9 10.3 - - - -
305B PHE* 2.8 46.2 + - + +
306B TYR* 3.5 6.8 - - - +
308B ARG* 1.3 83.1 - - - +
310B PRO* 1.4 60.4 - - - +
311B HIS* 2.8 27.7 + - + -
333B LEU* 4.6 2.7 - - + -
334B LEU* 3.7 27.8 - - + -
337B LEU* 4.0 9.4 - - + -
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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