Contacts of the helix formed by residues 272 - 285 (chain A) in PDB entry 4A69
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 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A ASP* 2.5 31.0 + - - -
261A LEU* 3.6 1.7 - - - +
270A ASN 3.9 1.2 + - - -
271A LEU* 1.3 75.4 - - - +
273A ILE* 1.3 65.5 + - - +
274A ARG* 3.5 8.9 + - - +
275A GLY 2.9 12.8 + - - -
276A HIS* 3.1 22.7 + - - +
342A VAL* 3.9 12.1 - - - -
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Residues in contact with ILE 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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261A LEU* 4.0 26.2 - - + +
272A SER* 1.3 72.6 - - - +
274A ARG* 1.3 63.2 + - - +
276A HIS* 3.4 3.2 + - - +
277A GLY* 2.9 21.3 + - - -
302A ASN* 4.2 16.6 - - + +
305A ARG* 4.3 2.7 - - + +
306A CYS* 4.0 22.4 - - - +
309A TYR* 3.6 26.7 - - + -
310A GLU* 4.6 0.7 - - - +
338A LEU 3.8 8.5 - - - +
339A HIS* 3.8 17.5 - - + +
340A PRO* 3.7 37.6 + - + +
342A VAL* 4.3 11.5 - - + +
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Residues in contact with ARG 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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272A SER* 3.2 8.6 + - - +
273A ILE* 1.3 80.4 - - - +
275A GLY* 1.3 56.6 + - - +
277A GLY 3.3 1.6 + - - -
278A GLU* 2.9 33.0 + - + +
309A TYR* 3.6 26.6 + - - +
321A GLU* 3.6 27.7 + - - -
339A HIS* 3.7 37.4 + - + +
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Residues in contact with GLY 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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229A ASP* 3.4 30.2 + - - -
271A LEU* 5.2 4.9 - - - -
272A SER* 2.9 11.3 + - - -
274A ARG* 1.3 75.9 - - - +
276A HIS* 1.3 61.2 + - - +
278A GLU* 3.2 28.1 + - - +
279A CYS* 3.5 12.4 + - - -
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Residues in contact with HIS 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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169A ILE* 3.2 20.3 - - + +
229A ASP* 4.6 0.2 + - - -
256A CYS* 3.4 25.4 - - + -
257A GLY 2.8 21.9 + - - -
258A ALA* 3.9 1.3 - - - -
260A SER* 3.2 18.8 - - - -
261A LEU* 3.8 18.8 - - + -
271A LEU* 4.5 13.9 - - + +
272A SER 3.1 15.2 + - - +
273A ILE 3.6 4.5 - - - +
275A GLY* 1.3 74.6 - - - +
277A GLY* 1.3 62.1 + - - +
279A CYS* 3.3 23.5 + - - +
280A VAL* 3.6 6.4 + - + +
306A CYS* 3.5 12.6 - - - -
310A GLU* 2.5 39.9 + - - +
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Residues in contact with GLY 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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273A ILE 2.9 14.6 + - - -
274A ARG 3.7 3.4 - - - -
275A GLY 3.3 0.2 - - - -
276A HIS* 1.3 74.1 - - - +
278A GLU* 1.3 58.2 + - - +
279A CYS 3.2 0.4 - - - -
280A VAL* 3.2 2.1 + - - +
281A GLU* 2.9 26.9 + - - +
309A TYR* 4.1 2.9 - - - -
310A GLU* 3.2 23.4 + - - -
313A LEU* 3.4 22.5 - - - +
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Residues in contact with GLU 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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229A ASP* 5.1 2.1 - - - +
233A LYS* 2.8 47.5 + - + +
237A GLN* 4.5 9.5 - - - +
274A ARG* 2.9 15.6 + - - +
275A GLY* 3.2 20.6 + - - +
277A GLY* 1.3 76.4 - - - +
279A CYS* 1.3 57.9 + - - +
281A GLU* 4.0 12.5 - - - +
282A TYR* 3.1 29.3 + - - +
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Residues in contact with CYS 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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169A ILE* 4.3 13.7 - - + -
232A TYR* 3.7 35.0 - - - -
233A LYS* 6.0 2.2 - - - -
236A PHE* 3.8 32.0 - - + -
254A LEU* 5.1 1.8 - - + -
271A LEU* 5.5 1.8 - - - -
275A GLY 3.7 13.2 - - - -
276A HIS* 3.3 12.7 + - - +
277A GLY 3.2 0.2 - - - -
278A GLU* 1.3 75.8 - - - +
280A VAL* 1.3 65.4 + - + +
282A TYR* 3.4 2.4 + - - +
283A VAL* 3.1 29.3 + - - +
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Residues in contact with VAL 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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169A ILE* 6.2 1.1 - - + -
254A LEU* 4.0 17.2 - - + +
256A CYS* 4.0 21.5 - - - -
276A HIS* 3.7 7.9 - - + +
277A GLY 3.2 6.4 + - - +
279A CYS* 1.3 74.0 - - + +
281A GLU* 1.3 60.1 + - - +
283A VAL* 3.3 4.9 + - - +
284A LYS* 3.0 26.3 + - - +
290A LEU* 5.2 0.7 - - - +
292A VAL* 5.2 1.3 - - + -
310A GLU* 3.5 42.2 - - + +
313A LEU* 5.3 2.9 - - + -
314A LEU* 3.7 35.6 - - + +
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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 GLY 2.9 16.5 + - - +
278A GLU* 4.1 12.4 - - - +
280A VAL* 1.3 78.2 - - - +
282A TYR* 1.3 56.1 + - - +
284A LYS* 3.2 15.4 + - + +
285A SER* 3.0 27.3 + - - -
313A LEU* 3.7 39.4 - - + +
314A LEU* 6.0 0.2 - - - -
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Residues in contact with TYR 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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236A PHE* 4.3 11.0 - + + -
237A GLN* 3.5 61.5 + - + +
240A ILE* 4.3 6.3 - - + -
241A ASN* 3.3 30.1 + - - +
278A GLU 3.1 20.2 + - - +
279A CYS* 3.7 6.7 - - - +
280A VAL 3.3 0.2 - - - -
281A GLU* 1.3 72.1 - - - +
283A VAL* 1.3 66.0 + - - +
285A SER* 2.6 32.6 + - - -
286A PHE* 3.3 33.9 - + - -
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Residues in contact with VAL 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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167A ILE* 4.0 20.6 - - + -
236A PHE* 4.1 15.3 - - + -
240A ILE* 4.9 4.0 - - + -
252A ILE* 3.8 26.7 - - + +
254A LEU* 4.0 18.2 - - + -
279A CYS 3.1 16.2 + - - +
280A VAL 3.7 7.0 - - - +
282A TYR* 1.3 75.6 - - - +
284A LYS* 1.3 62.4 + - - +
285A SER 3.4 0.5 + - - -
286A PHE* 3.4 23.8 + - + +
287A ASN 4.6 0.5 + - - -
288A ILE 5.4 2.3 + - - +
290A LEU* 3.7 30.3 - - + +
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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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3A LYS* 3.8 20.9 - - - +
125A ILE* 4.3 17.0 - - + -
280A VAL 3.0 13.9 + - - +
281A GLU* 3.4 17.9 - - + +
283A VAL* 1.3 77.6 - - - +
285A SER* 1.3 62.3 + - - +
286A PHE 3.1 1.6 + - - -
287A ASN* 3.1 22.1 + - - +
288A ILE 5.0 0.2 + - - -
290A LEU* 4.3 9.6 - - + +
313A LEU 3.8 18.6 - - - +
314A LEU* 3.3 40.6 - - + -
316A GLU* 2.9 29.9 + - - -
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Residues in contact with SER 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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281A GLU 3.0 11.7 + - - -
282A TYR* 2.6 34.6 + - - -
284A LYS* 1.3 77.0 - - - +
286A PHE* 1.3 65.4 + - - +
287A ASN* 3.1 15.9 + - - -
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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