Contacts of the helix formed by residues 268 - 273 (chain A) 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 ASP 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A GLU 3.4 12.5 + - - +
265A ASP* 3.6 6.1 - - - +
267A VAL* 1.3 79.2 - - - +
269A TYR* 1.3 74.3 + - - +
271A ARG* 3.4 14.8 + - - +
272A TYR* 3.2 38.1 + - - -
287A SER* 3.4 10.6 + - - +
291A ASN* 3.4 27.2 + - - +
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Residues in contact with TYR 269 (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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10A PHE* 4.1 22.0 - + + -
268A ASP* 1.3 90.3 - - - +
270A ASN* 1.3 64.5 + - - +
272A TYR* 3.0 19.0 + + - +
273A VAL* 3.6 15.8 - - + +
283A LEU* 4.0 17.3 - - + -
286A ILE* 3.9 8.1 - - + -
287A SER* 3.1 33.6 + - - +
290A GLU* 2.6 36.3 + - - +
291A ASN* 3.6 19.6 + - - -
328A GLN* 4.1 13.9 + - - +
331A HIS* 4.1 9.8 - - + +
332A LYS* 4.6 10.6 - - + +
335A LEU* 4.0 22.9 - - + +
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Residues in contact with ASN 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLN* 3.0 8.0 + - - +
234A VAL* 3.5 38.5 + - + +
237A THR* 4.9 1.3 - - + -
266A ALA 3.2 23.2 - - - +
267A VAL* 3.2 8.6 + - + +
269A TYR* 1.3 77.3 + - - +
271A ARG* 1.3 61.2 + - - +
273A VAL* 3.1 1.5 + - - +
274A GLY* 3.0 29.8 + - - +
276A ILE* 6.0 0.2 - - - +
280A SER* 3.4 27.5 + - - +
283A LEU* 3.8 26.1 - - - +
284A SER* 3.5 8.1 + - - -
287A SER* 4.4 0.2 - - - -
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Residues in contact with ARG 271 (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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34A LEU 4.5 5.3 + - - -
38A GLY* 3.4 24.5 + - - +
39A GLN* 3.5 14.1 + - - +
40A THR* 2.8 42.6 + - - +
41A GLU 3.1 5.9 + - - +
237A THR* 3.4 22.9 + - + +
263A TYR* 6.0 0.6 - - - -
264A GLU* 3.1 30.3 + - - -
267A VAL* 3.1 26.8 + - - +
268A ASP* 3.5 17.3 + - - +
269A TYR 3.2 0.2 - - - -
270A ASN* 1.3 76.2 - - - +
272A TYR* 1.3 70.7 + - + +
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Residues in contact with TYR 272 (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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40A THR* 4.0 25.9 + - + -
41A GLU* 3.1 37.3 - - - +
268A ASP* 3.2 44.2 + - - -
269A TYR* 3.0 11.1 + + - +
271A ARG* 1.3 85.8 - - + +
273A VAL* 1.3 59.9 + - - +
335A LEU* 4.7 15.0 - - + -
338A ARG* 2.9 38.3 + - - +
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Residues in contact with VAL 273 (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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10A PHE* 5.0 1.8 - - + -
12A VAL* 3.7 30.5 - - + -
41A GLU 3.2 5.7 + - - -
42A MET* 3.8 0.5 - - - -
43A ALA* 2.9 32.0 + - + +
153A GLN 3.7 0.9 - - - +
154A GLY* 3.6 5.4 - - - -
155A ALA 4.0 4.7 - - - +
269A TYR 3.6 13.0 - - - +
270A ASN 3.1 3.3 + - - +
272A TYR* 1.3 86.2 - - - +
274A GLY* 1.3 64.1 + - - +
276A ILE* 3.7 28.3 - - + -
283A LEU* 4.2 16.2 - - + -
335A LEU* 3.9 16.8 - - + -
338A 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