Contacts of the helix formed by residues 223 - 227 (chain D) in PDB entry 1XFB
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 TYR 223 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A ARG* 4.3 10.8 - - - -
8D LEU* 3.8 11.9 - - + -
13D LYS* 3.3 67.0 + - + +
14D LYS* 5.2 0.7 + - - -
16D LEU* 4.3 9.9 - - + -
17D SER* 4.2 7.0 - - - -
179D GLN* 2.8 37.5 + - - +
221D HIS 3.6 3.1 + - - +
222D VAL* 1.3 68.7 - - - +
224D LEU* 1.3 65.7 + - - +
225D GLU* 3.2 39.0 - - + +
226D GLY* 3.0 31.7 + - - -
227D THR* 3.1 4.4 - - - +
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Residues in contact with LEU 224 (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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259A ARG* 3.7 29.2 - - + +
214D TYR* 3.6 31.6 - - + +
217D LEU* 4.0 20.6 - - + -
218D SER 6.0 0.2 - - - +
222D VAL* 3.2 12.8 + - + +
223D TYR* 1.3 70.1 - - - +
225D GLU* 1.3 69.0 + - - +
226D GLY 2.8 4.7 + - - -
227D THR* 2.7 29.3 + - - +
262D PRO* 3.8 25.6 - - + -
264D ALA* 4.1 9.2 - - + -
265D VAL* 4.1 6.4 - - + -
266D PRO* 3.7 7.1 - - - +
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Residues in contact with GLU 225 (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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255A THR* 4.6 3.6 - - - +
258A ARG* 5.5 3.7 + - - +
259A ARG* 3.1 35.5 + - - +
17D SER* 3.5 24.9 + - - +
20D ALA* 4.1 0.7 - - - +
223D TYR* 3.2 42.8 - - + +
224D LEU* 1.3 86.8 + - - +
226D GLY* 1.3 55.3 + - - +
227D THR 3.5 1.3 - - - -
264D ALA* 3.3 30.8 - - + +
266D PRO* 3.8 15.5 - - + +
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Residues in contact with GLY 226 (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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16D LEU* 4.0 17.5 - - - +
20D ALA* 4.6 1.3 - - - -
179D GLN* 3.0 14.3 + - - +
184D VAL* 3.3 15.5 - - - +
185D PRO* 3.2 13.2 - - - +
223D TYR* 3.0 23.1 + - - -
224D LEU 2.8 1.4 + - - -
225D GLU* 1.3 78.4 - - - +
227D THR* 1.3 60.9 + - - +
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Residues in contact with THR 227 (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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20D ALA* 4.4 0.5 - - - +
179D GLN* 3.5 7.9 - - - +
184D VAL* 3.9 3.1 - - - -
185D PRO* 3.6 19.5 - - + -
187D VAL* 4.8 9.4 - - + -
214D TYR* 5.1 2.4 + - - -
217D LEU* 5.5 1.4 - - + +
222D VAL* 3.6 20.2 - - + -
223D TYR 3.1 20.2 - - - +
224D LEU* 2.7 26.4 + - + +
226D GLY* 1.3 82.4 - - - +
228D LEU* 1.3 69.5 + - - +
265D VAL* 4.4 8.2 - - - +
266D PRO* 3.1 27.2 - - - +
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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