Contacts of the helix formed by residues 300 - 314 (chain B) in PDB entry 1CYY
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 300 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298B GLY 3.8 3.0 + - - -
299B PHE* 1.3 75.9 - - - +
301B VAL* 1.3 67.2 + - - -
302B LYS* 3.3 17.5 - - - -
303B LYS* 3.1 12.7 + - - +
304B THR* 3.0 19.3 + - - -
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Residues in contact with VAL 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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290B GLN* 3.5 47.6 - - + +
299B PHE 3.9 0.4 + - - -
300B GLY* 1.3 70.3 - - - -
302B LYS* 1.3 70.9 + - - +
304B THR* 3.2 7.3 + - - -
305B MET* 2.9 33.9 + - + +
474B PRO 6.5 1.3 - - - -
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Residues in contact with LYS 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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300B GLY* 3.5 11.1 - - - -
301B VAL* 1.3 101.9 - - - +
303B LYS* 1.3 61.4 + - + +
305B MET* 4.0 4.7 - - - +
306B MET* 3.0 39.4 + - + +
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Residues in contact with LYS 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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298B GLY 5.5 0.7 - - - +
299B PHE* 3.8 32.9 - - + -
300B GLY 3.1 14.8 + - - +
302B LYS* 1.3 81.0 - - + +
304B THR* 1.3 65.6 + - - +
306B MET* 3.4 7.7 + - - +
307B MET* 3.0 35.5 + - + +
386B ASP* 3.0 33.2 + - - -
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Residues in contact with THR 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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289B LEU* 4.0 22.2 - - + -
290B GLN* 4.3 16.7 + - + -
293B ALA* 3.3 22.3 - - + +
299B PHE* 3.2 26.8 + - - +
300B GLY 3.0 12.9 + - - -
301B VAL* 3.6 9.8 - - - -
303B LYS* 1.3 76.9 - - - +
305B MET* 1.3 54.6 + - - +
307B MET 3.1 1.6 + - - -
308B ALA* 2.7 36.0 + - - +
390B LEU* 3.5 16.9 - - + +
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Residues in contact with MET 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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286B THR* 3.9 13.9 - - + +
289B LEU* 5.4 3.4 - - - -
290B GLN* 3.2 33.4 - - - +
301B VAL* 2.9 24.7 + - + +
302B LYS* 4.0 4.9 - - - +
304B THR* 1.3 79.0 - - - +
306B MET* 1.3 57.0 + - - +
308B ALA* 3.4 5.8 - - - +
309B GLN* 2.8 31.2 + - - +
320B MET* 3.8 33.8 - - + +
321B ARG* 4.0 24.2 - - + +
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Residues in contact with MET 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LYS* 3.0 31.3 + - + +
303B LYS* 3.7 8.1 - - - +
305B MET* 1.3 77.6 - - - +
307B MET* 1.3 65.4 + - + +
309B GLN* 3.5 7.4 + - + +
310B ARG* 3.1 43.4 + - - +
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Residues in contact with MET 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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299B PHE* 4.7 3.4 - - + -
303B LYS* 3.0 30.0 + - + +
306B MET* 1.3 77.5 - - - +
308B ALA* 1.3 60.5 + - - +
310B ARG* 3.2 22.8 + - - +
311B LEU* 2.9 31.4 + - - +
384B GLU* 3.2 33.4 - - + +
386B ASP* 3.3 23.6 - - + +
387B ALA* 2.7 44.4 - - + +
390B LEU* 3.6 20.0 - - + -
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Residues in contact with ALA 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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289B LEU* 4.7 10.8 - - + -
304B THR 2.7 17.3 + - - +
305B MET* 3.4 11.0 - - - +
307B MET* 1.3 74.4 - - - +
309B GLN* 1.3 57.0 + - - +
311B LEU* 2.9 5.0 + - - +
312B TYR* 2.8 34.7 + - - +
317B ILE* 3.6 9.9 - - + +
320B MET* 3.6 27.8 - - + -
390B LEU* 3.5 12.5 - - + +
394B ILE* 5.9 0.2 - - + -
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Residues in contact with GLN 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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305B MET 2.8 21.1 + - - +
306B MET* 3.7 7.9 - - - +
308B ALA* 1.3 72.4 - - - +
310B ARG* 1.3 57.2 + - - +
312B TYR* 3.4 8.8 + - - +
313B GLU* 3.0 71.2 + - - +
319B TYR* 5.6 0.6 - - - -
320B MET* 3.3 34.9 - - + +
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Residues in contact with ARG 310 (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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306B MET* 3.1 38.5 + - - +
307B MET* 3.3 18.8 - - - +
308B ALA 3.0 0.2 - - - -
309B GLN* 1.3 74.6 - - - +
311B LEU* 1.3 64.4 + - - +
313B GLU* 3.6 7.3 + - - +
314B ALA* 3.3 24.4 + - - +
382B ASP 6.0 1.1 - - - +
383B MET* 3.4 23.1 - - + -
384B GLU* 2.7 38.1 + - + +
387B ALA* 4.9 1.8 - - + -
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Residues in contact with LEU 311 (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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307B MET 2.9 16.9 + - - +
308B ALA 2.9 6.5 + - - +
310B ARG* 1.3 76.1 - - - +
312B TYR* 1.3 60.5 + - - +
314B ALA* 3.5 2.5 + - - +
315B GLY 3.4 2.9 + - - -
316B TYR* 3.0 38.6 + - + +
317B ILE* 3.7 17.3 - - + -
380B LEU* 4.1 17.5 - - + -
383B MET* 3.3 22.2 - - + -
387B ALA* 3.3 28.3 - - + +
390B LEU* 4.2 15.9 - - + -
391B TYR* 3.7 23.8 - - + +
394B ILE* 4.2 9.9 - - + -
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Residues in contact with TYR 312 (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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308B ALA 2.8 15.7 + - - +
309B GLN* 3.6 14.4 - - - +
311B LEU* 1.3 71.9 - - - +
313B GLU* 1.3 63.0 + - + +
314B ALA 2.9 4.3 - - - -
315B GLY* 2.5 29.0 + - - -
317B ILE* 3.4 28.4 - - + +
318B THR* 4.3 1.3 - - - +
319B TYR* 3.7 45.0 - + + +
320B MET* 3.6 24.9 - - - -
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Residues in contact with GLU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B GLN* 3.0 51.1 + - - +
310B ARG* 4.2 7.2 - - - +
312B TYR* 1.3 86.7 - - + +
314B ALA* 1.3 57.0 + - - +
315B GLY 3.2 1.0 + - - -
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Residues in contact with ALA 314 (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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310B ARG 3.3 17.0 + - - +
311B LEU 3.7 0.4 - - - +
312B TYR 2.8 1.2 + - - -
313B GLU* 1.3 76.3 - - - +
315B GLY* 1.3 61.9 + - - +
316B TYR* 3.4 37.3 + - + -
381B LYS* 4.3 12.7 - - - +
383B MET* 3.9 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