Contacts of the helix formed by residues 258 - 263 (chain R) in PDB entry 1RZZ
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 GLN 258 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162R TYR 5.0 0.8 + - - -
163R THR 3.6 12.9 + - - -
164R TYR* 3.5 6.8 - - - +
165R GLY* 3.2 34.7 - - - +
255R TRP* 3.3 9.9 - - - -
257R ASP* 1.3 78.6 - - + +
259R TRP* 1.3 61.0 + - - +
260R VAL* 3.1 13.7 - - + +
261R ASP* 2.8 41.6 + - - +
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Residues in contact with TRP 259 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164R TYR* 3.2 26.2 + - + +
166R ASN 4.5 2.9 - - - +
167R PHE* 3.6 26.4 - + - -
169R TYR* 3.6 19.8 - - + +
170R ASN* 3.3 30.8 - - + +
171R PRO* 3.4 27.6 - - + -
250R ILE* 3.6 24.7 - - + -
251R THR* 3.4 25.2 + - - +
255R TRP* 3.3 49.2 - + + +
257R ASP 3.4 2.8 + - - -
258R GLN* 1.3 71.0 - - - +
260R VAL* 1.3 64.2 + - - +
262R TRP* 2.9 41.2 + + + +
263R TRP* 3.6 7.1 - - - -
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Residues in contact with VAL 260 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164R TYR 4.8 1.7 + - - +
165R GLY* 6.0 0.4 - - - -
166R ASN 5.0 4.4 + - - +
169R TYR* 3.4 49.7 - - + +
258R GLN* 3.8 21.5 - - + +
259R TRP* 1.3 77.4 - - - +
261R ASP* 1.3 72.8 + - - +
262R TRP 3.4 0.3 + - - -
263R TRP* 3.5 18.5 + - - +
264R GLN* 4.6 4.3 + - - +
91S PHE* 6.1 4.5 - - + -
180S PHE* 6.2 0.9 - - + -
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Residues in contact with ASP 261 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255R TRP* 4.3 6.6 - - + -
257R ASP* 5.3 4.1 - - + +
258R GLN* 2.8 35.6 + - - +
260R VAL* 1.3 83.1 - - - +
262R TRP* 1.3 64.4 + - - +
263R TRP 3.1 2.2 - - - -
264R GLN* 3.0 35.3 + - + +
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Residues in contact with TRP 262 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171R PRO* 3.7 37.2 - - + -
255R TRP* 3.5 43.2 - + + -
259R TRP* 2.9 27.7 + + + +
261R ASP* 1.3 77.1 - - - +
263R TRP* 1.3 95.0 + + - +
264R GLN 3.0 4.0 + - - -
265R TRP* 2.9 64.4 + + - +
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Residues in contact with TRP 263 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169R TYR* 2.8 39.9 + + - -
171R PRO* 4.2 9.0 - - + -
174R MET* 3.3 36.3 - - + -
259R TRP 3.6 9.2 - - - -
260R VAL 3.5 17.7 - - - +
261R ASP 3.1 1.0 - - - -
262R TRP* 1.3 102.8 - + - +
264R GLN* 1.3 65.1 + - - +
265R TRP* 3.0 10.3 + + - -
266R TRP* 3.2 22.8 + + + +
267R VAL* 3.6 12.0 + - - +
90S PHE* 4.4 19.3 - + - -
91S PHE* 4.7 7.7 - + + -
180S PHE* 3.5 31.2 - + + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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