Contacts of the helix formed by residues 256 - 264 (chain A) in PDB entry 3UAJ
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 256 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 2.9 40.3 + - + +
218A LEU* 3.7 24.7 - - + +
237A MET* 4.7 3.4 - - + -
253A LEU* 3.4 27.9 - - + +
255A SER* 1.3 70.1 + - - +
257A GLU* 1.4 62.4 + - - +
258A GLY 3.4 2.0 - - - -
259A ALA* 3.3 18.8 + - + +
260A MET* 3.2 27.3 + - + +
258B GLY* 2.9 31.5 + - - +
262B SER* 3.1 22.2 + - - -
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Residues in contact with GLU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 4.0 10.1 - - + +
62A GLU* 5.6 1.2 - - - +
201A MET* 3.8 22.5 - - + +
202A LYS* 3.4 34.4 + - - +
255A SER* 3.2 18.7 + - - +
256A GLN* 1.4 78.0 - - - +
258A GLY* 1.3 56.6 + - - +
260A MET* 3.5 4.0 + - - +
261A HIS* 2.8 50.2 + - + -
254B GLY* 5.7 3.3 - - - -
255B SER* 5.5 3.1 - - - +
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Residues in contact with GLY 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A SER 4.5 0.4 + - - -
256A GLN 3.4 0.2 - - - -
257A GLU* 1.3 75.6 - - - +
259A ALA* 1.4 63.2 + - - +
261A HIS* 3.5 3.1 + - - +
262A SER* 3.4 19.4 + - - -
253B LEU 3.5 13.9 - - - -
255B SER 3.4 22.0 + - - +
256B GLN* 3.0 29.7 - - - +
259B ALA* 4.6 0.2 - - - -
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Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A GLN* 3.3 33.0 + - + +
257A GLU 3.3 0.4 - - - -
258A GLY* 1.4 77.2 - - - +
260A MET* 1.3 61.9 + - + +
262A SER* 3.8 7.6 + - - -
263A ALA* 3.7 17.2 + - - +
255B SER 4.7 0.2 + - - -
259B ALA* 3.8 34.9 - - + +
262B SER* 5.5 0.4 - - - +
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Residues in contact with MET 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 4.5 9.4 - - + -
125A ILE* 5.0 6.5 - - + -
199A MET* 3.7 33.7 - - + -
201A MET* 3.7 26.7 - - + -
212A TRP* 3.7 20.9 - - + -
216A LEU* 4.1 26.9 - - + -
218A LEU* 4.8 10.8 - - + -
256A GLN* 3.2 16.4 + - + +
257A GLU 3.8 0.2 - - - +
258A GLY 3.3 0.2 - - - -
259A ALA* 1.3 77.9 - - - +
261A HIS* 1.4 51.9 + - - +
262A SER 3.2 0.2 - - - -
263A ALA* 3.0 8.1 + - - +
264A LEU* 2.8 47.3 + - + +
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Residues in contact with HIS 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A MET* 3.9 17.4 - - - +
206A TRP* 4.5 19.5 - + - -
257A GLU* 2.8 47.0 + - + -
258A GLY 3.5 6.2 + - - +
260A MET* 1.4 76.2 - - - +
262A SER* 1.3 59.6 + - - +
264A LEU* 3.5 13.4 + - + +
265A ALA* 3.5 12.3 + - - +
252B VAL 5.1 5.1 + - - -
253B LEU* 2.9 47.8 + - + +
254B GLY* 5.2 2.2 - - - -
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Residues in contact with SER 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A GLY 3.4 4.5 + - - -
259A ALA* 3.8 10.8 - - - -
260A MET 3.2 0.8 - - - -
261A HIS* 1.3 75.8 - - - +
263A ALA* 1.3 60.8 + - - +
265A ALA* 3.5 18.9 - - - +
253B LEU* 3.8 12.6 - - - +
256B GLN* 3.2 27.5 + - - -
259B ALA* 5.5 0.6 - - - +
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A TRP* 3.8 32.3 - - + +
259A ALA 3.7 9.1 + - - +
260A MET* 3.0 11.3 + - - +
262A SER* 1.3 75.5 - - - +
264A LEU* 1.3 58.9 + - - +
265A ALA 3.3 5.2 + - - -
266A GLY 4.5 4.4 + - - -
267A ALA* 4.9 3.8 + - - +
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A MET* 4.0 17.5 - - + -
201A MET* 4.6 3.8 - - - -
206A TRP* 3.6 64.4 + - + +
208A VAL* 3.7 26.5 - - + -
212A TRP* 4.7 8.7 - - + -
260A MET* 2.8 33.7 + - + +
261A HIS* 3.5 10.5 + - - +
262A SER 3.4 0.4 - - - -
263A ALA* 1.3 76.5 - - - +
265A ALA* 1.4 60.7 + - - +
266A GLY 3.3 2.9 - - - -
267A ALA* 3.3 21.4 - - + +
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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