Contacts of the helix formed by residues 265 - 271 (chain H) in PDB entry 1ZWS
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 THR 265 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200H MET* 3.4 5.6 - - - -
263H ARG 4.5 3.6 - - - +
264H LEU* 1.3 75.9 - - - +
266H ILE* 1.3 58.8 + - - +
267H GLN* 3.1 18.7 + - - +
268H GLU* 2.8 35.0 + - + +
269H ALA* 2.6 32.4 + - - +
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Residues in contact with ILE 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 3.5 44.9 - - + +
127H VAL* 3.9 17.7 - - + -
128H ASN* 3.8 36.1 - - + +
131H HIS* 4.2 28.3 - - + -
200H MET* 3.2 22.4 - - - +
203H ILE* 5.6 0.4 - - + -
265H THR* 1.3 73.1 + - - +
267H GLN* 1.3 83.5 + - + +
269H ALA* 2.7 15.2 + - - +
270H LEU* 2.8 15.1 + - + +
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Residues in contact with GLN 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H ASN* 3.7 21.4 + - - +
265H THR* 3.1 8.3 + - - +
266H ILE* 1.3 91.4 - - + +
268H GLU* 1.3 64.6 + - + +
270H LEU* 3.3 12.9 + - - +
271H ARG* 3.0 37.0 + - - +
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Residues in contact with GLU 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262H LYS 5.3 0.9 - - - +
263H ARG 4.2 1.8 - - - +
264H LEU* 3.1 38.0 - - + +
265H THR* 2.8 34.5 + - + +
267H GLN* 1.3 77.3 - - + +
269H ALA* 1.3 68.1 + - - +
270H LEU 3.0 1.2 + - - -
271H ARG* 3.1 30.3 + - - +
272H HIS* 3.4 10.2 + - - +
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Residues in contact with ALA 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H LEU* 4.5 9.9 - - + -
200H MET* 3.4 27.6 - - + -
203H ILE* 6.3 0.2 - - + -
251H PHE* 3.3 32.3 - - + -
255H LEU* 4.5 1.3 - - + -
264H LEU* 4.1 14.5 - - + +
265H THR 2.6 9.1 + - - -
266H ILE* 2.7 10.1 + - - +
268H GLU* 1.3 72.7 - - - +
270H LEU* 1.3 61.3 + - - +
272H HIS* 3.2 16.4 - - - +
275H ILE* 3.7 4.5 - - - +
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Residues in contact with LEU 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H LYS* 4.4 16.2 - - + -
124H LEU* 3.4 39.9 - - + +
125H ASP* 4.7 8.5 - - - +
128H ASN* 4.1 35.4 - - + +
266H ILE* 2.8 13.8 + - + +
267H GLN* 3.5 17.9 - - - +
268H GLU 3.0 0.2 - - - -
269H ALA* 1.3 73.2 - - - +
271H ARG* 1.3 60.9 + - + +
272H HIS 2.9 11.1 + - - -
275H ILE* 3.2 21.9 - - + +
276H THR* 2.9 22.0 + - - +
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Residues in contact with ARG 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267H GLN* 3.0 33.4 + - - +
268H GLU* 3.1 29.2 + - - +
270H LEU* 1.3 77.9 - - + +
272H HIS* 1.3 58.1 + - - +
273H PRO* 3.7 6.8 - - - +
276H THR* 4.2 17.8 - - + +
278H VAL* 5.0 7.6 - - - +
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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