Contacts of the helix formed by residues 269 - 273 (chain D) in PDB entry 1XPM
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 269 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D PHE* 4.1 15.9 - + + -
268D ASP* 1.3 89.9 - - - +
270D ASN* 1.3 64.4 + - - +
272D TYR* 3.0 19.3 + + - +
273D VAL* 3.6 16.1 - - + +
283D LEU* 4.0 17.3 - - + -
286D ILE* 4.0 8.1 - - + -
287D SER* 3.1 33.1 + - - -
290D GLU* 2.6 35.8 + - - +
291D ASN* 3.5 21.9 + - - -
328D GLN* 4.1 12.0 + - - +
331D HIS* 4.1 15.6 - - + +
332D LYS* 4.5 10.9 - - + +
335D LEU* 4.0 22.9 - - + +
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Residues in contact with ASN 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D GLN* 3.0 15.2 + - - +
234D VAL* 3.5 39.3 + - + +
237D THR* 5.1 1.1 - - + -
266D ALA 3.2 23.2 - - - +
267D VAL* 3.2 7.9 + - - +
269D TYR* 1.3 75.7 + - - +
271D ARG* 1.3 60.9 + - - +
273D VAL* 4.5 1.3 - - - +
274D GLY* 3.0 23.2 + - - +
276D ILE* 6.0 0.2 - - - +
280D SER* 3.3 27.7 + - - +
283D LEU* 3.9 25.9 - - - +
284D SER* 3.5 7.6 + - - -
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Residues in contact with ARG 271 (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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34D LEU 4.5 5.3 + - - -
38D GLY* 3.4 24.5 + - - +
39D GLN* 3.4 12.9 + - - +
40D THR* 2.8 40.9 + - - +
41D GLU 3.1 5.2 + - - +
237D THR* 3.6 23.9 + - + +
263D TYR* 6.0 0.6 - - - -
264D GLU* 3.1 30.5 + - - -
267D VAL* 3.1 30.6 + - - +
268D ASP* 3.4 17.8 + - - +
269D TYR 3.1 0.4 - - - -
270D ASN* 1.3 76.8 - - - +
272D TYR* 1.3 71.8 + - + +
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Residues in contact with TYR 272 (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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40D THR* 4.0 23.2 + - + -
41D GLU* 3.1 40.4 - - + +
268D ASP* 3.2 43.6 + - - -
269D TYR* 3.0 12.4 + + - +
271D ARG* 1.3 85.9 - - + +
273D VAL* 1.3 60.1 + - - +
335D LEU* 4.8 15.0 - - + -
338D ARG* 2.9 38.3 + - - +
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Residues in contact with VAL 273 (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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10D PHE* 5.0 1.6 - - + -
12D VAL* 3.7 29.8 - - + -
41D GLU 3.2 5.7 + - - -
42D MET* 3.8 0.3 - - - -
43D ALA* 2.9 32.1 + - + +
153D GLN 3.7 0.9 - - - +
154D GLY* 3.6 5.7 - - - -
155D ALA 4.1 4.7 - - - +
269D TYR 3.6 13.2 - - - +
270D ASN 3.1 3.5 + - - +
272D TYR* 1.3 85.9 - - - +
274D GLY* 1.3 64.3 + - - +
276D ILE* 3.7 28.5 - - + -
283D LEU* 4.2 16.6 - - + -
335D LEU* 3.9 16.6 - - + -
338D ARG* 4.5 1.8 - - - +
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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