Contacts of the helix formed by residues 342 - 355 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B LYS* 6.3 2.2 - - - -
340B GLU* 5.6 1.3 - - - -
341B VAL* 1.3 78.3 - - - +
343B VAL* 1.3 60.1 + - - +
344B ASP* 3.5 10.1 + - - +
345B ALA* 3.1 24.9 + - - +
346B TYR* 2.8 27.3 + - - +
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Residues in contact with VAL 343 (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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17B VAL* 4.1 12.1 - - + +
21B LYS* 3.7 31.6 - - + +
22B LEU* 3.8 21.3 - - + +
25B ALA* 3.8 22.7 - - + -
26B ARG* 4.3 2.5 - - - +
341B VAL 3.9 0.2 + - - -
342B SER* 1.3 73.3 - - - +
344B ASP* 1.3 62.7 + - - +
346B TYR* 3.0 16.3 + - + +
347B GLU* 2.8 53.7 + - + +
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Residues in contact with ASP 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B SER* 3.2 9.5 + - - +
343B VAL* 1.3 81.3 - - - +
345B ALA* 1.3 61.5 + - - +
347B GLU* 3.3 16.8 + - - +
348B THR* 3.0 26.7 + - - -
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Residues in contact with ALA 345 (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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341B VAL* 4.0 10.8 - - + -
342B SER* 3.1 29.5 + - - +
344B ASP* 1.3 75.4 - - - +
346B TYR* 1.3 58.3 + - - +
348B THR* 3.2 8.5 + - - -
349B PHE* 2.9 42.2 + - + -
362B GLN* 5.9 0.2 - - - -
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Residues in contact with TYR 346 (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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17B VAL* 4.4 8.3 - - + -
22B LEU* 4.0 15.5 - - + -
26B ARG* 4.2 3.4 - - - -
42B MET* 4.3 13.4 - - - -
43B ALA 5.9 0.4 - - - -
44B VAL* 4.0 24.5 - - + -
145B LEU* 3.6 17.8 - - + +
150B GLU* 2.7 31.5 + - - +
153B GLN* 2.9 26.2 + - - -
341B VAL* 4.2 15.8 - - + +
342B SER 2.8 13.0 + - - +
343B VAL* 3.3 26.9 - - + +
345B ALA* 1.3 76.5 - - - +
347B GLU* 1.3 58.8 + - + +
349B PHE* 3.2 7.6 + - - +
350B PHE* 2.8 45.3 + + + +
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Residues in contact with GLU 347 (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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26B ARG* 2.8 32.1 + - - -
145B LEU* 4.0 22.4 - - + +
146B ASN* 5.0 3.8 + - - -
343B VAL* 2.8 30.9 + - + +
344B ASP* 3.3 15.8 + - - +
346B TYR* 1.3 83.9 - - + +
348B THR* 1.3 62.1 + - - +
350B PHE* 3.3 7.3 + - - +
351B LYS* 3.0 39.1 + - - +
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Residues in contact with THR 348 (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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344B ASP 3.0 14.1 + - - -
345B ALA* 3.2 11.8 + - - -
347B GLU* 1.3 75.8 - - - +
349B PHE* 1.3 65.4 + - - +
351B LYS* 3.5 7.1 + - - +
352B ARG* 3.1 29.7 + - + +
362B GLN* 3.6 29.4 - - - +
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Residues in contact with PHE 349 (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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15B TYR* 3.6 29.6 - + - -
44B VAL* 3.9 24.7 - - + -
45B SER 4.1 5.7 - - - +
46B PRO* 4.1 13.5 - - + -
47B VAL* 5.0 1.5 - - - +
341B VAL* 4.2 17.3 - - + -
345B ALA* 2.9 32.8 + - + -
346B TYR* 3.5 6.7 - - - +
348B THR* 1.3 76.0 - - - +
350B PHE* 1.3 65.7 + - - +
352B ARG* 3.2 23.1 + - - +
353B PHE* 2.9 24.5 + - - +
362B GLN* 3.5 32.8 - - + -
363B ASP* 3.4 22.7 - - - -
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Residues in contact with PHE 350 (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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44B VAL* 6.3 0.2 - - - -
142B ARG* 2.9 61.6 + - + +
144B GLY* 3.7 29.2 - - - -
145B LEU* 3.8 24.9 - - + -
153B GLN* 3.7 22.2 - - - -
193B TYR* 3.3 32.5 - + - -
346B TYR* 2.8 36.3 + + + +
347B GLU 3.5 6.3 - - - +
348B THR 3.2 0.2 - - - -
349B PHE* 1.3 76.0 - - - +
351B LYS* 1.3 63.2 + - + +
353B PHE* 3.2 7.0 + - - -
354B ASP* 3.3 8.7 + - - +
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Residues in contact with LYS 351 (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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145B LEU* 3.7 28.2 - - + +
347B GLU* 3.0 23.7 + - - +
348B THR* 4.0 6.5 - - - +
350B PHE* 1.3 76.8 - - + +
352B ARG* 1.3 63.2 + - + +
354B ASP* 3.4 26.5 + - - +
355B ASP* 3.8 10.0 + - - +
357B GLU* 4.1 5.1 - - - +
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Residues in contact with ARG 352 (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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47B VAL* 3.5 11.9 - - + +
348B THR* 3.1 23.8 + - + +
349B PHE* 3.2 15.5 + - - +
351B LYS* 1.3 77.6 - - + +
353B PHE* 1.3 62.3 + - - +
355B ASP 3.3 2.3 + - - -
356B VAL 3.0 3.6 + - - -
357B GLU* 2.9 71.9 + - + +
359B ASP* 3.3 30.3 - - - +
362B GLN* 2.8 47.5 + - - +
363B ASP* 3.0 40.4 + - - -
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Residues in contact with PHE 353 (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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45B SER* 3.6 25.4 - - - +
46B PRO 3.7 15.0 - - - -
47B VAL* 3.9 16.1 - - + +
49B GLN 3.4 25.4 - - - -
50B ASP* 4.9 7.9 - - + -
140B THR* 4.0 22.2 - - + -
142B ARG* 3.5 38.6 - - - +
349B PHE 2.9 13.2 + - - +
350B PHE* 3.2 9.2 + - - +
352B ARG* 1.3 75.6 - - - +
354B ASP* 1.3 66.5 + - - +
355B ASP 3.2 0.7 + - - -
356B VAL* 3.2 15.3 + - - +
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Residues in contact with ASP 354 (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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142B ARG* 2.9 18.6 + - - +
192B LYS* 5.4 3.9 - - + +
193B TYR* 3.0 31.6 + - - -
350B PHE* 3.3 16.8 - - - +
351B LYS* 3.4 19.4 - - - +
353B PHE* 1.3 80.8 - - - +
355B ASP* 1.3 68.9 + - - +
356B VAL* 3.9 2.9 + - - +
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Residues in contact with ASP 355 (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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351B LYS 3.8 8.6 + - - +
352B ARG 3.3 3.2 + - - -
353B PHE 3.2 0.2 - - - -
354B ASP* 1.3 86.6 - - - +
356B VAL* 1.3 75.5 + - - +
357B GLU* 3.2 26.5 + - + +
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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