Contacts of the helix formed by residues 299 - 307 (chain B) in PDB entry 4XJO
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 ALA 299 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B GLY 4.1 4.0 + - - -
116B ASP* 4.0 24.6 - - + +
117B THR* 5.0 3.4 - - + -
297B CYS 4.0 0.4 + - - -
298B THR* 1.3 73.9 - - - +
300B ASP* 1.3 57.1 + - - +
302B ALA* 3.2 6.1 + - - +
303B HIS* 2.8 57.2 + - + +
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Residues in contact with ASP 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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138B TYR* 3.0 29.0 + - - -
298B THR* 3.2 10.3 + - - +
299B ALA* 1.3 79.6 - - - +
301B VAL* 1.3 62.3 + - - +
303B HIS* 4.0 4.1 - - - +
304B THR* 2.9 40.2 + - - -
503B SO4 4.7 3.8 + - - -
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Residues in contact with VAL 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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134B MET* 4.4 12.8 - - + +
138B TYR* 3.7 24.6 - - + -
250B LEU* 4.0 24.2 - - + -
277B ASP* 4.4 11.4 - - + +
278B ILE* 4.5 5.4 - - + -
297B CYS* 3.8 20.4 - - + -
298B THR* 3.1 21.3 + - - +
300B ASP* 1.3 78.0 - - - +
302B ALA* 1.3 64.8 + - - +
304B THR* 3.9 1.2 - - - -
305B ILE* 3.0 46.4 + - + +
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Residues in contact with ALA 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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22A TRP* 3.6 29.7 - - + -
28A ILE* 3.9 10.5 - - + -
117B THR* 3.9 22.4 - - + +
297B CYS* 4.0 0.6 - - - -
298B THR 3.0 16.8 + - - +
299B ALA* 3.7 5.2 - - - +
301B VAL* 1.3 78.7 - - - +
303B HIS* 1.3 57.9 - - + +
305B ILE* 3.5 2.1 + - - +
306B SER* 2.8 33.8 + - - -
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Residues in contact with HIS 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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28A ILE* 3.9 32.3 - - + +
29A GLY* 5.4 3.1 - - - -
30A ARG* 3.3 16.3 + - - +
299B ALA* 2.8 44.9 + - + +
300B ASP* 4.1 3.7 - - - +
302B ALA* 1.3 74.4 - - + +
304B THR* 1.3 57.4 + - - +
306B SER* 3.3 3.3 + - - -
307B ALA* 2.9 27.4 + - - +
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Residues in contact with THR 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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138B TYR* 3.5 44.3 - - + +
141B GLY* 4.0 13.8 - - - +
142B ARG* 3.8 20.0 - - + -
300B ASP* 2.9 32.9 + - - -
303B HIS* 1.3 74.4 - - - +
305B ILE* 1.3 63.3 + - - +
307B ALA* 3.5 5.3 + - - +
308B GLY* 3.2 19.4 + - - -
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Residues in contact with ILE 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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22A TRP* 4.2 14.4 - - + -
134B MET* 3.6 44.6 - - + +
137B GLN* 3.9 21.9 + - + +
138B TYR* 4.0 12.3 - - - +
301B VAL* 3.0 34.7 + - + +
302B ALA 3.8 4.0 - - - +
304B THR* 1.3 75.6 - - - +
306B SER* 1.3 58.3 + - - +
308B GLY* 2.9 20.6 + - - -
311B GLY 4.3 0.3 + - - -
312B ALA 3.8 13.9 + - - +
313B LEU* 3.8 33.2 - - + +
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Residues in contact with SER 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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22A TRP* 4.1 4.2 - - - -
27A SER* 3.4 17.9 - - - +
28A ILE 2.9 34.2 + - - -
30A ARG* 3.5 21.8 - - - -
302B ALA 2.8 22.6 + - - -
303B HIS 3.3 4.5 + - - -
305B ILE* 1.3 76.9 - - - +
307B ALA* 1.3 57.6 + - - +
311B GLY* 3.3 28.6 - - - +
312B ALA 4.4 0.4 - - - +
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Residues in contact with ALA 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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30A ARG* 3.5 25.3 - - - +
141B GLY 5.8 1.3 - - - -
303B HIS 2.9 17.3 + - - +
304B THR* 3.8 5.8 - - - +
306B SER* 1.3 74.3 - - - +
308B GLY* 1.3 65.4 + - - +
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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