Contacts of the helix formed by residues 266 - 279 (chain A) in PDB entry 4Z2C
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 ASN 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A MET 3.8 7.2 - - - +
111A ASP* 2.7 41.1 + - - +
112A GLY* 3.4 10.5 - - - -
264A MET 4.3 0.6 + - - -
265A VAL* 1.3 73.2 - - - +
267A LYS* 1.3 74.6 + - - +
268A THR* 2.9 11.0 + - - -
269A LYS* 3.6 23.4 - - + +
270A VAL* 3.1 26.4 + - - +
322A GLN* 5.2 2.4 + - - -
11E T 5.2 11.1 + - - +
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Residues in contact with LYS 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A MET* 4.3 18.8 + - + +
111A ASP* 2.4 41.2 + - - +
261A PHE* 3.5 33.2 - - + -
265A VAL 3.6 4.1 + - - +
266A ASN* 1.3 73.3 + - - +
268A THR* 1.3 58.5 + - - +
270A VAL* 3.1 11.3 + - - +
271A HIS* 2.9 26.1 + - - +
291A ASP* 3.5 25.0 + - - +
293A SER* 3.3 30.2 + - - -
298A VAL* 3.7 25.1 - - + -
300A PHE* 4.5 7.5 - - + -
447C ARG* 4.5 1.6 - - - +
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Residues in contact with THR 268 (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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111A ASP* 3.3 34.0 - - - +
266A ASN* 2.9 10.5 + - - -
267A LYS* 1.3 77.0 - - - +
269A LYS* 1.3 57.7 - - - +
271A HIS* 3.1 12.1 + - + +
272A GLU* 2.9 30.6 + - + +
291A ASP* 5.0 5.5 + - - -
447C ARG* 5.9 1.2 + - - -
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Residues in contact with LYS 269 (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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266A ASN* 3.4 28.0 + - + +
267A LYS 3.3 0.4 - - - -
268A THR* 1.3 79.0 - - - +
270A VAL* 1.3 58.4 + - + +
272A GLU* 3.8 5.7 - - - +
273A HIS* 2.9 30.9 + - - +
322A GLN* 5.6 5.6 - - - +
10E T 5.9 2.9 - - - +
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Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A PHE* 3.9 18.6 - - + -
265A VAL* 3.7 22.0 - - + -
266A ASN 3.1 16.3 + - - +
267A LYS 3.1 8.0 + - - +
269A LYS* 1.3 74.8 - - + +
271A HIS* 1.3 59.9 + - - +
273A HIS* 3.7 5.6 - - - +
274A ILE* 2.9 38.2 + - + +
300A PHE* 4.3 4.0 - - + -
321A THR* 4.8 6.3 - - - +
322A GLN* 4.6 17.5 - - + +
323A MET* 3.8 29.8 - - + -
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Residues in contact with HIS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LYS 2.9 10.1 + - - +
268A THR* 3.3 16.2 - - + +
270A VAL* 1.3 77.9 - - - +
272A GLU* 1.3 57.6 + - - +
274A ILE* 3.3 2.3 + - - +
275A VAL* 2.9 45.6 + - + +
289A VAL* 3.3 43.9 + - + +
291A ASP* 4.9 14.2 + - + +
300A PHE* 3.6 26.7 - + + -
406C GLY* 4.7 7.7 - - - -
447C ARG* 5.7 2.7 - - - -
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Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 2.9 17.7 + - + +
269A LYS* 3.8 7.2 - - - +
271A HIS* 1.3 74.6 - - - +
273A HIS* 1.3 60.3 + - - +
275A VAL* 3.3 6.8 + - - +
276A ARG* 2.9 31.6 + - - +
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Residues in contact with HIS 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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269A LYS 2.9 18.6 + - - +
270A VAL* 3.7 6.5 - - - +
272A GLU* 1.3 75.8 - - - +
274A ILE* 1.3 57.6 + - - +
276A ARG* 3.4 8.0 + - - +
277A LEU* 2.9 49.3 + - + +
320A MET 3.1 25.5 + - - -
321A THR* 3.8 20.9 - - + -
322A GLN* 4.7 4.5 - - + -
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Residues in contact with ILE 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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270A VAL* 2.9 22.6 + - + +
271A HIS* 3.6 4.7 - - - +
273A HIS* 1.3 74.0 - - - +
275A VAL* 1.3 61.1 + - - +
277A LEU* 3.1 9.7 + - - +
278A VAL* 2.9 27.2 + - + +
283A ILE* 5.9 0.2 - - - +
286A ILE* 4.3 17.9 - - + +
289A VAL* 4.0 26.5 - - + -
300A PHE* 3.9 20.2 - - + -
302A ILE* 5.7 3.4 - - + -
317A LEU* 3.9 25.8 - - + -
321A THR* 4.0 10.5 - - + -
323A MET* 3.7 28.7 - - + -
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Residues in contact with VAL 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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271A HIS* 2.9 46.7 + - + +
272A GLU* 3.6 6.7 - - - +
274A ILE* 1.3 75.6 - - - +
276A ARG* 1.3 60.1 + - - +
278A VAL* 3.0 7.1 + - - +
279A GLN* 2.9 31.7 + - + +
289A VAL* 4.9 3.8 - - + -
407C LEU* 4.0 42.1 - - + +
408C GLU 5.3 2.5 - - - +
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Residues in contact with ARG 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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272A GLU 2.9 17.0 + - - +
273A HIS* 3.7 9.6 - - - +
275A VAL* 1.3 78.1 - - - +
277A LEU* 1.3 57.7 + - + +
278A VAL 3.6 0.2 + - - -
279A GLN* 4.0 4.0 + - - +
280A GLU* 3.2 31.3 + - - +
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Residues in contact with LEU 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 HIS* 2.9 43.3 + - + +
274A ILE* 3.1 6.9 + - - +
276A ARG* 1.3 77.8 - - + +
278A VAL* 1.3 60.3 + - - +
280A GLU* 3.8 6.2 + - - +
281A LYS 3.7 1.2 + - - -
282A ARG* 3.2 60.4 + - + +
283A ILE* 3.3 14.1 + - + -
317A LEU* 5.6 2.2 - - + -
320A MET* 3.9 26.0 - - + -
321A THR* 3.8 24.2 - - + -
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Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ILE* 2.9 15.4 + - + +
275A VAL* 3.0 4.5 + - - +
277A LEU* 1.3 75.3 - - - +
279A GLN* 1.3 56.3 + - - +
280A GLU 3.0 10.0 + - - -
281A LYS* 3.2 12.1 + - - -
283A ILE* 4.0 15.2 - - + +
286A ILE* 4.8 19.7 - - + -
407C LEU* 3.7 25.6 - - + -
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Residues in contact with GLN 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A VAL* 2.9 18.5 + - + +
276A ARG* 4.2 4.0 - - - +
278A VAL* 1.3 72.9 - - - +
280A GLU* 1.3 58.0 + - - +
281A LYS 3.7 0.2 - - - -
407C LEU* 4.9 15.7 - - + +
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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