Contacts of the helix formed by residues 271 - 285 (chain A) in PDB entry 3CVW
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 SER 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ARG* 3.5 29.0 + - - +
19A HIS* 3.1 24.3 + - - -
20A ASP* 2.5 31.1 + - - -
138A SER 4.6 0.2 + - - -
265A LEU* 4.3 0.7 - - - -
270A LEU* 1.3 71.7 - - - +
272A ALA* 1.3 60.8 + - - +
273A ARG* 3.5 8.1 + - - +
274A LEU* 3.5 7.6 + - - +
275A PHE* 2.9 28.1 + - - +
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Residues in contact with ALA 272 (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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138A SER 5.2 1.0 + - - -
139A HIS 4.0 11.0 + - - +
141A ILE* 4.0 14.8 - - + +
265A LEU* 3.9 17.5 - - + -
270A LEU 3.4 4.8 + - - -
271A SER* 1.3 72.2 + - - +
273A ARG* 1.3 53.5 + - + +
275A PHE* 4.2 3.8 - - - -
276A ASN* 2.8 35.0 + - - +
300A LEU* 3.5 14.5 - - + +
303A ARG* 3.4 28.7 - - - +
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Residues in contact with ARG 273 (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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20A ASP* 3.1 32.1 + - - +
22A PRO* 4.0 12.1 - - - +
137A CYS 2.7 27.5 + - - -
138A SER* 3.4 35.1 - - - +
140A THR 3.9 6.3 + - - +
141A ILE* 4.0 29.7 + - + +
171A VAL* 6.2 2.2 - - + -
172A PRO* 3.4 39.2 - - + +
173A LYS 4.2 9.4 + - - -
174A VAL* 3.6 15.4 - - + +
175A LEU* 6.1 0.2 - - - +
271A SER* 3.2 0.4 - - - -
272A ALA* 1.3 77.7 - - - +
274A LEU* 1.3 56.8 + - - +
276A ASN* 3.4 4.4 + - - +
277A GLN* 2.9 29.1 + - - +
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Residues in contact with LEU 274 (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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19A HIS* 3.6 29.4 - - + +
174A VAL* 3.8 28.6 - - + +
175A LEU 5.7 1.1 - - - +
228A LEU* 4.1 16.2 - - + -
231A MET* 4.6 7.6 - - + -
270A LEU* 4.6 8.5 - - + -
271A SER* 3.2 15.8 + - - +
273A ARG* 1.3 75.5 - - - +
275A PHE* 1.3 57.3 + - - +
277A GLN* 3.1 11.0 + - - +
278A LYS* 2.7 60.3 + - + +
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Residues in contact with PHE 275 (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 MET* 3.6 29.2 - - + -
234A SER* 5.9 1.1 - - - -
235A LEU* 4.2 20.4 - - + -
259A THR* 4.8 4.7 - - + -
261A LEU* 3.7 28.5 - - + -
265A LEU* 4.8 7.2 - - + -
270A LEU* 4.4 11.2 - - + -
271A SER 2.9 16.1 + - - +
272A ALA* 3.7 6.1 - - - +
274A LEU* 1.3 76.1 - - - +
276A ASN* 1.3 56.9 + - - +
278A LYS* 3.5 1.4 + - - +
279A LEU* 3.0 48.9 + - + +
296A LEU* 3.7 28.7 - - + -
300A LEU* 3.7 33.4 - - + -
521A FAD 4.5 8.3 - + - -
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Residues in contact with ASN 276 (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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141A ILE* 3.8 34.7 - - + +
142A TYR* 5.5 2.4 + - - -
171A VAL* 4.6 12.1 - - - +
272A ALA 2.8 22.6 + - - +
273A ARG* 3.4 6.0 + - - +
275A PHE* 1.3 73.1 - - - +
277A GLN* 1.3 57.1 + - - +
279A LEU* 3.3 5.3 + - - +
280A LYS* 3.0 50.7 + - - +
297A ILE* 3.4 28.1 - - - +
300A LEU* 3.8 9.4 - - + +
301A MET* 4.3 4.1 - - - +
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Residues in contact with GLN 277 (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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171A VAL* 6.2 1.8 - - - +
172A PRO 5.3 2.0 + - - -
173A LYS* 5.5 1.0 - - - +
174A VAL* 3.5 41.5 + - + +
273A ARG 2.9 17.4 + - - +
274A LEU* 3.1 12.3 + - + +
276A ASN* 1.3 76.0 - - - +
278A LYS* 1.3 62.5 + - + +
280A LYS* 3.5 14.0 + - + +
281A GLU* 3.3 42.6 + - + +
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Residues in contact with LYS 278 (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 MET* 4.0 19.1 - - + -
232A GLU* 3.7 24.5 + - - +
235A LEU* 3.7 22.0 - - + -
274A LEU* 2.7 39.5 + - + +
275A PHE* 3.8 5.4 - - - +
277A GLN* 1.3 71.2 - - - +
279A LEU* 1.3 63.3 + - - +
281A GLU* 3.5 20.6 + - - +
282A ILE* 3.4 27.7 + - - +
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Residues in contact with LEU 279 (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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235A LEU* 3.9 13.0 - - + -
241A VAL* 3.7 27.9 - - + +
275A PHE* 3.0 51.9 + - + +
276A ASN* 3.7 5.4 - - - +
278A LYS* 1.3 75.5 - - - +
280A LYS* 1.3 64.5 + - - +
282A ILE* 3.3 7.9 + - - +
283A ILE* 3.1 28.7 + - + +
296A LEU* 4.1 23.3 - - + +
297A ILE* 3.8 38.1 - - + +
300A LEU* 4.4 6.3 - - + -
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Residues in contact with LYS 280 (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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171A VAL* 4.0 32.3 - - - +
276A ASN* 3.0 41.4 + - - +
277A GLN* 3.7 12.5 - - + +
279A LEU* 1.3 75.7 - - - +
281A GLU* 1.3 62.1 + - + +
283A ILE* 3.3 10.0 + - - +
284A LYS* 3.2 47.6 + - - +
297A ILE* 4.6 9.8 - - + +
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Residues in contact with GLU 281 (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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277A GLN* 3.3 32.9 + - + +
278A LYS* 3.7 23.7 + - - +
279A LEU 3.3 0.4 - - - -
280A LYS* 1.3 78.3 - - + +
282A ILE* 1.3 60.9 + - - +
284A LYS* 3.4 14.9 + - + +
285A ARG* 3.4 38.0 + - - +
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Residues in contact with ILE 282 (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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235A LEU* 3.8 49.6 - - + +
238A GLU* 3.6 39.5 - - + +
241A VAL* 4.1 17.3 - - + -
242A ALA* 4.8 2.9 - - + +
278A LYS 3.4 13.6 + - - +
279A LEU 3.3 7.7 + - - +
281A GLU* 1.3 74.0 - - - +
283A ILE* 1.3 67.7 + - + +
285A ARG* 3.0 35.7 + - - +
286A GLN* 3.0 15.3 + - + +
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Residues in contact with ILE 283 (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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241A VAL* 5.2 4.5 - - + +
242A ALA* 4.2 17.9 - - - +
279A LEU* 3.1 16.8 + - + +
280A LYS* 3.5 9.6 - - - +
282A ILE* 1.3 76.8 - - + +
284A LYS* 1.3 59.5 + - + +
286A GLN* 2.8 30.2 + - - +
289A HIS* 3.5 52.8 + - + +
290A SER 4.8 3.8 - - - +
297A ILE* 3.6 25.8 - - + -
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Residues in contact with LYS 284 (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 LYS* 3.2 39.7 + - - +
281A GLU* 3.7 14.1 - - + +
282A ILE 3.2 0.2 - - - -
283A ILE* 1.3 79.4 - - + +
285A ARG* 1.3 61.4 + - + +
286A GLN 3.4 1.0 - - - -
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Residues in contact with ARG 285 (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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238A GLU* 2.9 38.9 + - - +
281A GLU* 3.4 21.9 + - - +
282A ILE* 3.0 33.2 + - - +
284A LYS* 1.3 79.5 - - + +
286A GLN* 1.3 68.8 + - - +
287A PRO* 3.9 6.6 - - - +
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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