Contacts of the helix formed by residues 266 - 271 (chain A) in PDB entry 1Z6T
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 ASP 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A VAL 5.7 0.2 - - - +
246A TRP* 5.0 7.3 - - - +
264A THR* 2.9 19.8 + - - +
265A ARG* 1.3 79.1 - - + +
267A LYS* 1.3 60.2 + - - +
268A SER* 2.8 40.2 + - - -
269A VAL* 3.1 23.4 + - + +
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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
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151A THR* 5.0 6.1 - - + +
153A HIS* 3.9 45.5 + - + +
264A THR* 4.0 10.2 - - - +
265A ARG 4.1 1.8 + - - -
266A ASP* 1.3 73.6 + - - +
268A SER* 1.3 62.5 + - - +
269A VAL* 3.2 3.7 + - - +
270A THR* 3.7 19.8 + - - +
271A ASP* 5.0 0.2 - - - +
279A VAL* 5.3 8.1 - - + -
214B GLN* 5.9 3.0 - - - +
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Residues in contact with SER 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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248A SER* 4.3 3.5 - - - -
266A ASP* 2.8 27.1 + - - -
267A LYS* 1.3 77.0 - - - +
269A VAL* 1.3 57.2 + - - +
270A THR 3.0 11.3 + - - -
271A ASP* 3.1 38.0 + - - +
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Residues in contact with VAL 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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151A THR* 5.3 0.7 - - + -
245A VAL* 3.9 9.2 - - + +
246A TRP 3.6 34.1 - - - +
247A ASP* 3.8 5.2 - - - +
248A SER* 3.1 34.3 - - - +
251A LEU* 3.2 13.9 - - + +
262A LEU* 3.9 26.2 - - + -
264A THR* 3.7 18.2 - - + +
266A ASP* 3.3 26.2 - - + +
267A LYS 3.2 1.3 - - - +
268A SER* 1.3 75.5 + - - +
270A THR* 1.3 58.8 + - - +
271A ASP 3.3 1.8 - - - -
272A SER* 4.7 0.5 + - - -
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Residues in contact with THR 270 (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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149A TRP* 4.3 8.8 - - - +
151A THR* 4.5 14.7 + - - +
251A LEU* 3.7 14.5 - - - +
267A LYS 3.7 15.9 - - - +
268A SER 3.0 2.0 + - - -
269A VAL* 1.3 78.9 - - - +
271A ASP* 1.3 62.5 + - - +
272A SER 3.4 2.5 - - - -
273A VAL* 3.3 25.1 + - - +
277A LYS* 2.7 55.1 + - + +
279A VAL* 6.1 4.7 - - + -
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Residues in contact with ASP 271 (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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248A SER* 4.6 3.1 - - - +
268A SER* 3.1 35.4 + - - +
269A VAL 3.3 1.2 - - - -
270A THR* 1.3 84.2 - - - +
272A SER* 1.3 59.2 + - - +
273A VAL 3.2 4.5 + - - +
277A LYS* 4.4 5.7 + - - +
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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