Contacts of the helix formed by residues 342 - 355 (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 SER 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A VAL* 4.5 0.2 - - - -
21A LYS* 6.2 2.7 - - - -
340A GLU* 5.4 2.9 - - - -
341A VAL* 1.3 76.9 - - - +
343A VAL* 1.3 60.3 + - - +
344A ASP* 3.5 9.7 + - - +
345A ALA* 3.2 23.4 + - - +
346A TYR* 2.9 26.6 + - - +
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Residues in contact with VAL 343 (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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17A VAL* 4.2 10.5 - - + +
21A LYS* 3.6 37.6 - - + +
22A LEU* 3.8 11.2 - - + +
25A ALA* 3.8 22.7 - - + -
26A ARG* 4.2 11.2 - - - +
342A SER* 1.3 74.1 - - - +
344A ASP* 1.3 60.6 + - - +
346A TYR* 3.2 16.5 + - + +
347A GLU* 2.9 47.6 + - + +
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Residues in contact with ASP 344 (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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342A SER* 3.2 9.3 + - - +
343A VAL* 1.3 79.5 - - - +
345A ALA* 1.3 61.8 + - - +
347A GLU* 3.3 16.3 + - - +
348A THR* 3.0 26.2 + - - -
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Residues in contact with ALA 345 (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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341A VAL* 4.1 11.0 - - + -
342A SER* 3.2 26.1 + - - +
344A ASP* 1.3 78.4 - - - +
346A TYR* 1.3 57.7 + - - +
348A THR* 3.1 9.1 + - - -
349A PHE* 2.9 42.3 + - + -
362A GLN* 5.8 0.2 - - - -
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Residues in contact with TYR 346 (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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17A VAL* 4.4 12.1 - - + -
22A LEU* 4.1 12.3 - - + -
26A ARG* 4.1 7.0 - - - -
42A MET* 4.3 13.0 - - - -
43A ALA 6.0 0.2 - - - -
44A VAL* 4.0 22.0 - - + -
145A LEU* 3.5 18.4 - - + +
150A GLU* 2.7 32.2 + - + +
153A GLN* 2.9 29.6 + - - -
341A VAL* 4.1 15.8 - - + +
342A SER 2.9 13.4 + - - +
343A VAL* 3.2 20.8 + - + +
345A ALA* 1.3 77.4 - - - +
347A GLU* 1.3 61.0 + - + +
349A PHE* 3.2 7.9 + - - +
350A PHE* 2.8 38.6 + + + +
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Residues in contact with GLU 347 (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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26A ARG* 2.7 32.1 + - - -
145A LEU* 4.0 24.0 - - + +
146A ASN* 4.6 4.7 - - - +
343A VAL* 2.9 28.8 + - + +
344A ASP* 3.3 14.3 + - - +
346A TYR* 1.3 86.9 - - + +
348A THR* 1.3 61.7 + - - +
350A PHE* 3.7 7.0 - - - +
351A LYS* 3.0 39.9 + - - +
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Residues in contact with THR 348 (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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344A ASP 3.0 14.9 + - - -
345A ALA* 3.1 12.4 + - - -
347A GLU* 1.3 76.3 - - - +
349A PHE* 1.3 65.1 + - - +
351A LYS* 4.0 6.0 - - - +
352A ARG* 3.1 34.5 + - + +
362A GLN* 3.5 30.1 - - - +
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Residues in contact with PHE 349 (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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15A TYR* 3.6 23.6 - + - -
44A VAL* 4.0 25.6 - - + -
45A SER 4.0 7.8 - - - +
46A PRO* 4.1 11.9 - - + -
47A VAL* 4.9 1.3 - - - +
341A VAL* 4.1 24.5 - - + -
345A ALA* 2.9 30.2 + - + -
346A TYR* 3.5 6.1 - - - +
348A THR* 1.3 76.3 - - - +
350A PHE* 1.3 56.4 + - - +
352A ARG* 3.2 23.0 + - - +
353A PHE* 2.9 30.9 + - - +
362A GLN* 3.5 33.4 - - + -
363A ASP* 3.4 22.2 - - - -
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Residues in contact with PHE 350 (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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44A VAL* 5.6 0.2 - - - +
45A SER 5.7 0.2 - - - -
142A ARG* 2.8 61.4 + - + +
144A GLY* 3.7 30.1 - - - -
145A LEU* 3.9 25.8 - - + -
153A GLN* 3.6 20.6 - - - -
193A TYR* 3.4 32.3 - + - -
346A TYR* 2.8 35.4 + + + +
347A GLU 3.7 5.8 - - - +
349A PHE* 1.3 77.6 - - - +
351A LYS* 1.3 62.8 + - + +
353A PHE* 3.3 2.5 + - - -
354A ASP* 3.0 13.7 + - - +
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Residues in contact with LYS 351 (chain A).
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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145A LEU* 3.6 28.3 - - + -
347A GLU* 3.0 25.1 + - - +
348A THR* 4.0 6.5 - - - +
350A PHE* 1.3 76.2 - - + +
352A ARG* 1.3 62.5 + - + +
354A ASP* 3.4 25.3 + - - +
355A ASP* 3.5 14.0 - - - +
357A GLU* 4.3 2.1 - - - +
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Residues in contact with ARG 352 (chain A).
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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47A VAL* 3.3 10.0 - - + +
348A THR* 3.1 23.5 + - + +
349A PHE* 3.4 15.7 - - - +
351A LYS* 1.3 73.9 - - + +
353A PHE* 1.3 66.7 + - - +
355A ASP 3.2 2.3 + - - -
356A VAL* 3.0 3.5 + - - -
357A GLU* 2.9 72.8 + - + +
359A ASP* 3.3 29.0 - - - +
362A GLN* 2.8 48.7 + - - +
363A ASP* 3.0 40.8 + - - -
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Residues in contact with PHE 353 (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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45A SER* 3.7 27.6 - - - +
46A PRO 3.7 12.1 - - - -
47A VAL* 3.9 17.0 - - + +
49A GLN 3.4 25.8 - - - -
50A ASP* 4.9 7.4 - - + -
140A THR* 4.1 22.0 - - + -
142A ARG* 3.4 39.0 - - - +
349A PHE 2.9 16.6 + - - +
350A PHE* 3.5 5.8 - - - +
351A LYS 3.3 0.2 - - - -
352A ARG* 1.3 77.2 - - - +
354A ASP* 1.3 62.4 + - - +
356A VAL* 3.1 18.3 + - + +
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Residues in contact with ASP 354 (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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142A ARG* 3.0 15.7 + - - +
192A LYS* 5.0 14.6 - - + +
193A TYR* 3.0 34.6 + - - -
350A PHE* 3.0 21.0 + - - +
351A LYS* 3.5 18.5 - - - +
352A ARG 3.2 0.4 - - - -
353A PHE* 1.3 79.8 - - - +
355A ASP* 1.3 69.1 + - - +
356A VAL* 4.9 2.6 - - - +
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Residues in contact with ASP 355 (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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351A LYS 3.5 11.7 - - - +
352A ARG 3.2 3.0 + - - -
353A PHE 3.1 0.4 - - - -
354A ASP* 1.3 86.3 - - - +
356A VAL* 1.3 74.8 + - - +
357A GLU* 2.9 35.2 + - + +
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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