Contacts of the helix formed by residues 342 - 355 (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 SER 342 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D VAL* 4.5 0.2 - - - -
21D LYS* 6.1 3.1 - - - -
340D GLU* 5.3 3.4 - - - -
341D VAL* 1.3 77.0 - - - +
343D VAL* 1.3 61.0 + - - +
344D ASP* 3.5 9.2 + - - +
345D ALA* 3.1 23.9 + - - +
346D TYR* 2.8 26.3 + - - +
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Residues in contact with VAL 343 (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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17D VAL* 4.2 10.3 - - + +
21D LYS* 3.6 37.1 - - + +
22D LEU* 3.8 11.4 - - + +
25D ALA* 3.8 22.7 - - + -
26D ARG* 4.2 6.5 - - - +
342D SER* 1.3 73.7 - - - +
344D ASP* 1.3 61.3 + - - +
346D TYR* 3.1 20.5 + - + +
347D GLU* 2.8 50.6 + - + +
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Residues in contact with ASP 344 (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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342D SER* 3.2 9.3 + - - +
343D VAL* 1.3 81.2 - - - +
345D ALA* 1.3 61.0 + - - +
347D GLU* 3.2 16.2 + - - +
348D THR* 3.1 25.7 + - - -
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Residues in contact with ALA 345 (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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341D VAL* 4.0 11.0 - - + -
342D SER* 3.1 25.5 + - - +
344D ASP* 1.3 78.4 - - - +
346D TYR* 1.3 57.3 - - - +
348D THR* 3.1 9.2 + - - -
349D PHE* 2.9 42.0 + - + -
362D GLN* 5.8 0.2 - - - -
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Residues in contact with TYR 346 (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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17D VAL* 4.4 11.4 - - + -
22D LEU* 4.1 14.8 - - + -
26D ARG* 4.2 3.1 - - - -
42D MET* 4.2 13.2 - - - -
43D ALA 6.0 0.2 - - - -
44D VAL* 4.0 22.2 - - + -
145D LEU* 3.6 20.1 - - + +
150D GLU* 2.7 31.2 + - - +
153D GLN* 2.9 30.2 + - - -
341D VAL* 4.1 15.8 - - + +
342D SER 2.8 13.9 + - - +
343D VAL* 3.1 21.7 + - + +
345D ALA* 1.3 76.9 - - - +
347D GLU* 1.3 61.6 + - + +
349D PHE* 3.3 8.2 + - - +
350D PHE* 2.9 38.7 + + + +
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Residues in contact with GLU 347 (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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26D ARG* 2.7 32.7 + - - -
145D LEU* 4.0 18.1 - - + +
146D ASN* 4.9 3.8 + - - -
343D VAL* 2.8 29.2 + - + +
344D ASP* 3.6 13.3 - - - +
345D ALA 3.2 0.2 - - - -
346D TYR* 1.3 87.1 - - + +
348D THR* 1.3 60.9 + - - +
350D PHE* 3.7 7.4 - - - +
351D LYS* 3.0 49.3 + - - +
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Residues in contact with THR 348 (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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344D ASP 3.1 13.5 + - - -
345D ALA* 3.1 13.3 + - - -
347D GLU* 1.3 75.6 - - - +
349D PHE* 1.3 64.4 + - - +
351D LYS* 3.4 8.4 + - - +
352D ARG* 3.1 34.3 + - + +
362D GLN* 3.6 30.3 - - - +
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Residues in contact with PHE 349 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D TYR* 3.6 23.8 - + - -
44D VAL* 4.0 24.7 - - + -
45D SER 4.1 7.7 - - - +
46D PRO* 4.1 11.9 - - + -
47D VAL* 4.8 0.9 - - - +
341D VAL* 4.1 23.8 - - + -
345D ALA* 2.9 30.9 + - + -
346D TYR* 3.6 6.7 - - - +
348D THR* 1.3 75.9 - - - +
350D PHE* 1.3 57.2 + - - +
352D ARG* 3.2 22.2 + - - +
353D PHE* 2.9 31.6 + - - +
362D GLN* 3.4 35.7 - - + -
363D ASP* 3.4 22.2 - - - -
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Residues in contact with PHE 350 (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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44D VAL* 5.6 0.2 - - - +
45D SER 5.7 0.2 - - - -
142D ARG* 2.9 63.6 + - + +
144D GLY* 3.8 22.0 - - - -
145D LEU* 4.0 21.8 - - + -
153D GLN* 3.6 20.4 - - - -
193D TYR* 3.4 38.1 - + - -
346D TYR* 2.9 36.3 + + + +
347D GLU* 3.7 9.0 - - - +
349D PHE* 1.3 77.8 - - - +
351D LYS* 1.3 61.1 + - + +
353D PHE* 3.3 2.1 + - - -
354D ASP* 3.0 13.8 + - - +
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Residues in contact with LYS 351 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145D LEU* 3.2 21.7 - - + +
347D GLU* 3.0 46.5 + - - +
348D THR* 3.9 7.3 - - - +
350D PHE* 1.3 74.1 - - + +
352D ARG* 1.3 65.2 + - + +
354D ASP* 3.4 24.3 + - - +
355D ASP* 3.6 13.7 - - - +
357D GLU* 4.0 3.2 - - - +
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Residues in contact with ARG 352 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D VAL* 3.4 10.8 - - + +
348D THR* 3.1 22.6 + - + +
349D PHE* 3.5 15.1 - - - +
351D LYS* 1.3 77.4 - - + +
353D PHE* 1.3 59.2 + - - +
355D ASP 3.3 2.3 + - - -
356D VAL* 3.0 8.3 + - - -
357D GLU* 2.8 72.7 + - + +
359D ASP* 3.3 27.8 - - - +
362D GLN* 2.8 47.6 + - - +
363D ASP* 2.9 41.8 + - - -
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Residues in contact with PHE 353 (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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45D SER* 3.7 24.2 - - - +
46D PRO 3.7 15.0 - - - -
47D VAL* 3.8 16.8 - - + +
49D GLN 3.5 25.4 - - - -
50D ASP* 4.9 8.1 - - + -
140D THR* 4.1 21.1 - - + -
142D ARG* 3.4 39.9 - - - +
349D PHE 2.9 16.2 + - - +
350D PHE* 3.6 5.8 - - - +
351D LYS 3.2 0.2 - - - -
352D ARG* 1.3 78.3 - - - +
354D ASP* 1.3 62.8 + - - +
356D VAL* 3.1 18.4 + - + +
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Residues in contact with ASP 354 (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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142D ARG* 3.0 20.0 + - - +
192D LYS* 5.0 14.5 - - + +
193D TYR* 3.0 34.3 + - - -
350D PHE* 3.0 19.7 + - - +
351D LYS* 3.5 14.5 - - - +
352D ARG 3.3 0.4 - - - -
353D PHE* 1.3 78.8 - - - +
355D ASP* 1.3 68.8 + - - +
356D VAL* 4.9 2.6 - - - +
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Residues in contact with ASP 355 (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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351D LYS 3.6 12.2 + - - +
352D ARG 3.3 2.6 + - - -
353D PHE 3.1 0.4 - - - -
354D ASP* 1.3 84.6 - - - +
356D VAL* 1.3 73.8 + - - +
357D GLU* 3.1 31.1 + - + +
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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