Contacts of the helix formed by residues 299 - 309 (chain B) in PDB entry 2XAR
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 GLY 299 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334A LYS* 5.7 2.7 - - - -
295B VAL 3.3 3.9 + - - -
296B TYR 3.2 11.7 + - - -
297B GLY 3.1 4.8 - - - -
298B SER* 1.3 79.1 + - - +
300B VAL* 1.3 62.0 + - - +
301B LEU* 3.2 4.7 + - - -
302B ASP* 3.4 33.9 + - - +
303B ARG* 4.2 8.5 + - - +
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B HIS* 3.6 35.4 - - + +
295B VAL* 4.3 3.0 + - - +
298B SER* 3.0 22.2 + - - +
299B GLY* 1.3 76.1 - - - +
301B LEU* 1.3 79.8 + - + +
302B ASP 3.6 0.2 + - - -
303B ARG* 3.7 13.5 + - - +
304B LEU 3.6 8.0 + - - -
371B ILE* 4.4 6.7 - - + -
373B ILE* 6.1 0.4 - - + -
403B VAL* 3.9 24.0 - - + -
405B PHE* 3.4 36.9 - - + -
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B LEU* 3.4 42.0 - - + +
218B PHE* 3.5 31.8 - - + -
225B VAL* 5.8 0.2 - - + -
295B VAL* 3.5 32.7 + - + +
299B GLY* 3.2 1.3 - - - -
300B VAL* 1.3 88.4 - - + +
302B ASP* 1.3 63.2 + - - +
304B LEU* 3.1 5.2 + - + -
305B LEU* 2.8 31.5 + - - +
371B ILE* 3.3 34.8 - - + -
405B PHE* 5.7 0.2 - - + -
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Residues in contact with ASP 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A LYS* 4.4 16.8 + - - -
424A LYS* 6.0 4.9 - - - +
218B PHE 4.7 9.9 - - - +
220B GLY* 5.1 5.9 - - - -
299B GLY* 3.5 25.2 - - - +
300B VAL 3.3 0.6 - - - -
301B LEU* 1.3 81.2 - - - +
303B ARG* 1.3 63.2 + - + +
305B LEU* 3.4 11.4 + - - +
306B GLU* 3.2 28.5 + - - +
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Residues in contact with ARG 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LEU 5.0 1.9 - - - +
97B LEU* 3.3 39.4 + - + +
98B GLY* 4.5 6.5 - - - -
100B LYS* 4.7 10.9 - - - +
101B HIS* 3.2 38.3 + - - -
298B SER 5.6 4.0 + - - -
299B GLY 4.2 10.4 + - - +
300B VAL* 4.0 15.9 - - + +
301B LEU 3.3 0.4 - - - -
302B ASP* 1.3 73.7 - - + +
304B LEU* 1.3 66.0 + - - +
306B GLU* 3.4 18.6 + - - +
307B ILE* 3.2 21.1 + - - +
405B PHE* 5.6 0.9 - - + -
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 4.2 13.4 - - + +
169B PRO* 4.0 21.1 - - + -
218B PHE* 4.2 6.5 - - + -
300B VAL 3.6 5.2 + - - +
301B LEU* 3.1 9.7 + - + +
303B ARG* 1.3 74.5 - - - +
305B LEU* 1.3 66.3 - - - +
306B GLU 3.0 1.8 - - - -
307B ILE* 2.9 19.5 + - + +
308B GLN* 2.9 21.8 + - - +
366B ALA* 3.7 28.7 - - + +
369B CYS* 3.4 36.1 - - - -
371B ILE* 4.8 4.5 - - + -
405B PHE* 3.9 27.4 - - + -
408B LEU* 5.6 0.2 - - + -
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B GLY* 3.5 33.4 - - - +
173B PHE* 3.8 17.9 - - + -
218B PHE* 3.8 31.6 - - + +
301B LEU 2.8 16.7 + - - +
302B ASP* 3.6 9.6 - - - +
304B LEU* 1.3 75.1 - - - +
306B GLU* 1.3 57.6 + - - +
308B GLN* 3.2 15.3 + - - +
309B LYS* 2.8 53.1 + - + +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A LYS* 5.7 4.4 - - - -
428A SER* 6.0 3.5 - - - -
302B ASP* 3.2 18.6 + - - +
303B ARG* 3.4 16.3 - - - +
304B LEU 3.0 0.4 - - - -
305B LEU* 1.3 74.4 - - + +
307B ILE* 1.3 66.6 + - + +
309B LYS* 3.3 19.1 + - + +
310B LEU* 3.3 17.3 + - - +
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ILE* 5.1 4.5 - - + -
96B LEU* 3.3 48.2 - - + +
97B LEU* 3.6 26.7 - - + -
303B ARG 3.2 16.4 - - - +
304B LEU* 3.4 8.3 - - - +
306B GLU* 1.3 74.2 - - + +
308B GLN* 1.3 67.0 + - - +
310B LEU* 3.0 29.4 + - + +
362B ILE* 3.7 29.4 - - + +
363B ALA* 3.4 8.0 - - - -
366B ALA* 3.5 19.5 - - + -
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Residues in contact with GLN 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B LYS 3.0 21.3 + - - +
171B CYS* 3.3 8.1 - - - -
172B GLY 3.2 25.5 + - - -
173B PHE* 3.5 17.7 - - + -
218B PHE* 4.0 6.8 - - - -
304B LEU* 2.9 30.3 + - - +
305B LEU* 3.2 16.7 + - - +
307B ILE* 1.3 76.3 - - - +
309B LYS* 1.3 57.3 + - - +
310B LEU 2.9 6.3 + - - -
311B ASP* 3.0 14.9 + - - +
363B ALA* 3.2 14.2 - - - +
366B ALA* 3.1 35.2 + - + -
367B LYS* 3.5 14.2 - - + +
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Residues in contact with LYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A TYR* 4.5 6.3 + - - +
421A LYS* 5.3 12.5 - - - +
425A LYS* 6.2 5.8 - - + -
173B PHE* 3.5 49.1 - - + +
305B LEU* 2.8 48.1 + - + +
306B GLU* 3.3 13.7 + - + +
307B ILE 3.2 0.6 - - - -
308B GLN* 1.3 68.5 - - - +
310B LEU* 1.3 58.5 + - - +
311B ASP 3.0 14.0 + - - +
312B LYS* 3.8 9.5 + - - +
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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