Contacts of the helix formed by residues 259 - 263 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D TRP* 3.4 39.7 - - - +
164D PRO* 5.9 0.2 - - - +
170D ASN* 3.6 20.0 + - - -
257D GLY 3.3 0.8 - - - -
258D ILE* 1.3 86.8 + - - +
260D HIS* 1.3 55.9 + - - +
261D ALA 3.2 2.5 - - - -
262D TYR* 2.9 43.1 + - - -
263D MET* 3.7 2.8 + - - +
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Residues in contact with HIS 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ASN* 5.2 1.1 - - - +
412C ASP* 5.2 1.4 + - - -
481C ARG 3.3 18.3 + - - -
482C ARG* 3.5 22.5 - - + +
483C TYR* 3.3 29.6 + + - -
143D TRP* 3.8 2.6 - - - -
252D CYS* 3.2 31.7 - - - +
253D SER* 4.0 2.6 - - - -
254D GLU* 3.2 23.0 + - - -
255D LEU* 3.6 24.6 + - + -
256D CYS* 3.6 13.2 - - - -
257D GLY 3.3 16.8 + - - +
258D ILE 3.6 1.0 + - - -
259D SER* 1.3 74.7 - - - +
261D ALA* 1.3 56.4 + - - +
262D TYR 3.2 4.5 + - - -
263D MET* 4.0 2.3 + - - +
286D CU 2.0 31.1 - - - -
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Residues in contact with ALA 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C ARG 5.3 0.6 + - - +
483C TYR* 3.6 49.3 - - + -
484C ILE* 4.1 24.5 - - + -
485C ASP 4.1 6.9 - - - +
160D MET* 4.8 1.0 - - - +
191D LEU* 4.6 9.9 - - - +
251D GLN* 4.4 5.0 - - - +
258D ILE 5.2 1.2 + - - +
259D SER 3.2 1.4 - - - -
260D HIS* 1.3 76.9 - - - +
262D TYR* 1.3 72.6 + - + +
263D MET 3.8 1.5 + - - -
264D PRO* 6.1 0.2 - - - +
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Residues in contact with TYR 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C VAL* 3.7 9.9 - - - +
90C PRO* 3.4 25.7 - - + +
92C GLY* 5.3 3.1 - - - -
484C ILE* 3.4 29.0 - - + +
485C ASP* 3.8 7.3 + - + +
143D TRP* 4.3 7.3 - - - +
160D MET* 3.6 24.0 + - + +
163D SER* 5.0 2.9 - - - -
170D ASN* 3.5 60.7 + - + +
191D LEU* 3.6 24.0 - - + -
258D ILE 4.6 5.6 - - - -
259D SER* 2.9 28.3 + - - +
261D ALA* 1.3 93.7 - - + +
263D MET* 1.3 60.7 + - - +
264D PRO* 3.7 6.1 - - - -
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Residues in contact with MET 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C TYR* 5.6 0.2 + - - -
141D TYR 3.3 27.6 - - - +
143D TRP* 3.6 31.0 - - + +
144D TYR* 3.5 14.4 - - - +
145D TRP* 2.8 60.2 + - + +
158D SER 6.1 0.2 - - - -
160D MET* 4.9 2.0 - - - +
217D HIS* 3.5 10.5 - - + +
252D CYS* 3.6 18.1 + - + +
259D SER 3.8 9.4 - - - +
260D HIS 4.0 2.6 + - - +
261D ALA 3.8 2.0 - - - -
262D TYR* 1.3 80.0 - - - +
264D PRO* 1.4 61.9 - - - +
287D CU1 2.4 30.7 - - - -
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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