Contacts of the helix formed by residues 261 - 269 (chain B) in PDB entry 1HZW
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 HIS 261 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B ASP* 4.4 19.1 + - - -
220B GLY* 5.2 7.0 - - - -
221B LEU* 5.4 8.3 - - + -
257B ILE* 4.0 11.0 - - + -
258B TYR* 2.8 33.2 + + + +
260B ASN* 1.3 104.0 + - - +
262B ILE* 1.3 59.6 + - - +
264B PRO* 3.2 14.0 - - + +
265B LEU* 2.8 39.9 + - + +
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Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 3.4 24.4 - - + +
56B LEU* 3.4 35.9 - - + -
257B ILE* 3.6 19.5 - - + +
258B TYR 3.5 1.9 + - - +
259B LEU* 3.2 29.7 + - + +
261B HIS* 1.3 78.6 - - - +
263B GLU* 1.3 74.7 + - + +
265B LEU* 3.3 2.3 + - - +
266B LYS* 2.9 40.8 + - + +
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Residues in contact with GLU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B LEU 4.9 0.2 + - - -
260B ASN 5.3 0.2 - - - -
262B ILE* 1.3 90.0 - - + +
264B PRO* 1.3 74.1 - - + +
266B LYS* 3.0 27.7 + - - +
267B ILE* 3.0 31.4 + - + +
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Residues in contact with PRO 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B ASN 3.8 16.8 - - - +
261B HIS* 3.2 23.6 - - + +
263B GLU* 1.3 94.5 - - + +
265B LEU* 1.3 59.3 + - + +
267B ILE* 3.1 15.7 + - + +
268B GLN* 2.9 26.9 + - - +
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Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B TYR* 4.7 0.4 - - - +
37B ILE* 4.0 30.6 - - + +
41B LEU* 5.2 1.8 - - + -
220B GLY* 4.2 28.3 - - - +
257B ILE* 3.4 47.3 - - + -
261B HIS* 2.8 21.7 + - + +
262B ILE* 3.7 3.8 - - - +
264B PRO* 1.3 76.4 - - + +
266B LYS* 1.3 60.5 + - - +
268B GLN* 3.3 27.2 - - - +
269B LEU* 2.8 34.3 + - - +
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Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 3.5 23.6 - - + -
262B ILE* 2.9 36.9 + - + +
263B GLU* 3.0 30.8 + - - +
265B LEU* 1.3 77.2 - - - +
267B ILE* 1.3 63.0 + - + +
269B LEU* 3.3 19.9 + - + +
270B GLN* 3.1 19.7 + - - +
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Residues in contact with ILE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B GLU* 3.0 20.9 + - + +
264B PRO* 3.3 14.4 - - + +
266B LYS* 1.3 76.5 - - + +
268B GLN* 1.3 57.7 + - - +
270B GLN* 2.7 40.6 + - + +
271B ARG* 3.3 23.5 + - + +
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Residues in contact with GLN 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B TYR* 3.9 22.6 + - - -
34B LEU* 4.5 4.5 - - + +
37B ILE* 4.9 1.3 - - + +
74B LEU* 5.7 0.8 - - - +
76B THR* 2.9 52.8 + - - +
77B LYS* 3.8 27.5 - - - +
220B GLY 5.5 0.9 - - - +
224B PRO* 6.1 0.6 - - - +
264B PRO 2.9 13.3 + - - +
265B LEU* 3.2 31.0 + - + +
267B ILE* 1.3 79.0 - - - +
269B LEU* 1.3 56.1 + - - +
271B ARG* 2.9 42.5 + - - +
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 3.4 52.8 - - + +
37B ILE* 3.7 15.7 - - + -
38B GLN* 3.4 28.5 - - + +
41B LEU* 3.6 28.0 - - + -
265B LEU 2.8 20.5 + - - +
266B LYS* 3.4 12.8 - - + +
267B ILE 3.1 0.4 - - - -
268B GLN* 1.3 76.2 - - - +
270B GLN* 1.3 65.2 + - - +
271B ARG 3.3 5.2 - - - +
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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