Contacts of the helix formed by residues 259 - 263 (chain B) in PDB entry 3OMA
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 SER 259 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B DMU 5.4 3.2 + - - -
143B TRP* 3.5 38.8 - - - +
164B PRO* 6.0 0.3 - - - +
170B ASN* 3.8 18.2 + - - -
257B GLY 3.3 0.4 - - - -
258B ILE* 1.3 89.1 + - - +
260B HIS* 1.3 57.1 + - - +
261B ALA 3.1 2.0 - - - -
262B TYR* 2.8 44.0 + - - -
263B MET* 3.7 2.4 + - - +
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Residues in contact with HIS 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ASN* 5.1 1.3 - - - +
412A ASP* 5.1 0.8 + - - -
481A ARG 3.2 18.9 + - - -
482A ARG* 3.3 27.7 - - + +
483A TYR* 3.3 24.6 + + - -
143B TRP* 3.7 2.4 - - - -
252B CYS* 3.1 31.7 - - - +
253B SER* 4.2 1.5 - - - -
254B GLU 3.3 21.3 + - - -
255B LEU* 3.5 26.9 + - + -
256B CYS* 3.5 13.7 - - - -
257B GLY 3.2 17.2 + - - +
258B ILE 3.5 0.6 - - - -
259B SER* 1.3 75.9 - - - +
261B ALA* 1.3 57.2 + - - +
262B TYR 3.1 4.3 + - - -
263B MET* 4.0 2.3 + - - +
287B CU 2.1 30.9 - - - -
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Residues in contact with ALA 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ARG 5.4 0.4 - - - +
483A TYR* 3.8 41.2 - - + -
484A ILE* 4.0 29.8 - - + +
485A ASP 4.2 6.0 - - - +
160B MET* 4.7 1.0 - - - +
191B LEU* 4.4 9.5 - - - +
251B GLN* 4.5 5.5 - - - +
258B ILE 5.1 1.1 + - - +
259B SER* 3.1 1.2 - - - +
260B HIS* 1.3 77.6 - - - +
262B TYR* 1.3 75.8 + - + +
263B MET 3.8 1.1 + - - -
264B PRO* 5.5 0.2 - - - +
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Residues in contact with TYR 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL* 3.8 8.5 - - - +
90A PRO* 3.4 24.4 - - + +
92A GLY* 5.4 3.4 - - - -
484A ILE* 3.4 31.2 - - + +
485A ASP* 3.8 7.8 - - + +
143B TRP* 4.3 7.6 - - - +
160B MET* 3.6 28.1 + - + +
163B SER* 4.8 3.8 - - - -
170B ASN* 3.5 56.8 + - + +
191B LEU* 3.6 23.6 - - + -
258B ILE 4.6 6.1 - - - -
259B SER* 2.8 29.9 + - - +
261B ALA* 1.3 92.0 - - + +
263B MET* 1.3 60.3 + - - +
264B PRO* 3.7 6.3 - - - -
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Residues in contact with MET 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TYR 3.4 27.6 - - - +
143B TRP* 3.6 31.4 - - + +
144B TYR* 3.5 18.8 - - - +
145B TRP* 2.8 48.2 + - + +
158B SER 6.1 0.4 - - - -
160B MET* 4.9 2.7 - - - +
217B HIS* 3.5 8.5 - - + +
252B CYS* 3.6 19.0 + - + -
259B SER 3.8 9.4 - - - +
260B HIS 4.0 2.6 + - - +
261B ALA 3.8 1.6 - - - -
262B TYR* 1.3 79.1 - - - +
264B PRO* 1.4 63.5 - - - +
288B CU1 2.5 30.3 - - - -
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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