Contacts of the helix formed by residues 342 - 355 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C VAL* 4.6 0.4 - - - -
21C LYS* 5.7 6.5 - - - -
340C GLU* 5.5 2.2 - - - -
341C VAL* 1.3 77.1 - - - +
343C VAL* 1.3 59.8 + - - +
344C ASP* 3.5 9.9 + - - +
345C ALA* 3.1 24.6 + - - +
346C TYR* 2.8 27.6 + - - +
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Residues in contact with VAL 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C VAL* 4.1 11.9 - - + +
21C LYS* 3.6 31.6 - - + +
22C LEU* 3.8 21.3 - - + +
25C ALA* 3.8 22.2 - - + -
26C ARG* 4.3 2.5 - - - +
342C SER* 1.3 74.0 - - - +
344C ASP* 1.3 62.9 + - - +
346C TYR* 3.1 15.6 + - + +
347C GLU* 2.8 53.5 + - + +
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Residues in contact with ASP 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C SER* 3.2 8.8 + - - +
343C VAL* 1.3 82.8 - - - +
345C ALA* 1.3 61.2 + - - +
347C GLU* 3.3 15.0 + - - +
348C THR* 3.1 26.8 + - - -
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Residues in contact with ALA 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C VAL* 4.0 10.8 - - + -
342C SER* 3.1 29.7 + - - +
344C ASP* 1.3 75.6 - - - +
346C TYR* 1.3 58.2 + - - +
348C THR* 3.1 8.4 + - - -
349C PHE* 2.9 41.0 + - + -
362C GLN* 5.0 0.2 - - - +
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Residues in contact with TYR 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C VAL* 4.4 9.0 - - + -
22C LEU* 4.1 16.2 - - + -
26C ARG* 4.3 3.1 - - - -
42C MET* 4.3 12.8 - - - -
43C ALA 5.9 0.4 - - - -
44C VAL* 3.9 24.7 - - + -
145C LEU* 3.6 18.9 - - + +
150C GLU* 2.7 31.1 + - - +
153C GLN* 3.0 25.7 + - - -
341C VAL* 4.2 15.6 - - + +
342C SER 2.8 13.7 + - - +
343C VAL* 3.3 26.2 - - + +
345C ALA* 1.3 76.5 - - - +
347C GLU* 1.3 61.1 + - + +
349C PHE* 3.2 7.4 + - - +
350C PHE* 2.8 44.2 + + + +
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Residues in contact with GLU 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ARG* 2.8 32.4 + - - -
145C LEU* 4.0 22.6 - - + +
146C ASN* 4.8 4.0 - - - +
343C VAL* 2.8 31.8 + - + +
344C ASP* 3.7 13.6 - - - +
345C ALA 3.3 0.2 - - - -
346C TYR* 1.3 83.2 - - + +
348C THR* 1.3 62.7 + - - +
350C PHE* 3.3 7.3 + - - +
351C LYS* 3.1 41.2 + - - +
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Residues in contact with THR 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344C ASP 3.1 15.0 + - - -
345C ALA* 3.1 11.6 + - - -
347C GLU* 1.3 75.3 - - - +
349C PHE* 1.3 65.4 + - - +
351C LYS* 3.4 8.5 + - - +
352C ARG* 3.1 30.0 + - + +
362C GLN* 3.5 28.3 - - - +
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Residues in contact with PHE 349 (chain C).
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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15C TYR* 3.6 29.2 - + - -
44C VAL* 3.9 24.2 - - + -
45C SER 4.1 5.9 - - - +
46C PRO* 4.1 13.2 - - + -
47C VAL* 4.9 1.3 - - - +
341C VAL* 4.2 17.7 - - + -
345C ALA* 2.9 32.6 + - + -
346C TYR* 3.5 6.5 - - - +
348C THR* 1.3 76.0 - - - +
350C PHE* 1.3 65.3 + - - +
352C ARG* 3.2 23.5 + - - +
353C PHE* 2.9 24.5 + - - +
362C GLN* 3.5 32.5 - - + -
363C ASP* 3.4 22.4 - - - -
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Residues in contact with PHE 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL* 6.3 0.2 - - - -
142C ARG* 2.9 61.1 + - + +
144C GLY* 3.7 29.2 - - - -
145C LEU* 3.9 22.0 - - + -
153C GLN* 3.6 22.4 - - - -
193C TYR* 3.4 31.0 - + - -
346C TYR* 2.8 37.4 + + + +
347C GLU* 3.5 9.2 - - - +
348C THR 3.2 0.2 - - - -
349C PHE* 1.3 77.1 - - - +
351C LYS* 1.3 62.5 + - + +
353C PHE* 3.3 2.4 + - - -
354C ASP* 3.1 14.8 + - - +
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Residues in contact with LYS 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C LEU* 3.8 27.1 - - + -
347C GLU* 3.1 25.9 + - - +
348C THR* 3.9 6.5 - - - +
350C PHE* 1.3 73.7 - - + +
352C ARG* 1.3 66.9 + - + +
354C ASP* 3.3 26.4 + - - +
355C ASP* 3.8 9.9 + - - +
357C GLU* 4.4 4.8 - - - +
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Residues in contact with ARG 352 (chain C).
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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47C VAL* 3.5 12.0 - - + +
348C THR* 3.1 19.9 + - + +
349C PHE* 3.2 19.3 + - - +
351C LYS* 1.3 77.8 - - + +
353C PHE* 1.3 61.7 + - - +
355C ASP 3.3 2.6 + - - -
356C VAL 3.0 3.1 + - - -
357C GLU* 2.9 71.8 + - + +
359C ASP* 3.3 29.6 - - - +
362C GLN* 2.9 42.7 + - - +
363C ASP* 3.0 40.8 + - - -
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Residues in contact with PHE 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C SER* 3.6 24.9 - - - +
46C PRO 3.6 15.7 - - - -
47C VAL* 3.8 16.8 - - + +
49C GLN 3.4 25.4 - - - -
50C ASP* 4.9 7.9 - - + -
140C THR* 4.0 21.5 - - + -
142C ARG* 3.5 41.1 - - - +
349C PHE 2.9 16.3 + - - +
350C PHE* 3.6 5.6 - - - +
351C LYS 3.2 0.2 - - - -
352C ARG* 1.3 75.6 - - - +
354C ASP* 1.3 66.5 + - - +
355C ASP 3.1 0.7 + - - -
356C VAL* 3.2 15.1 + - - +
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Residues in contact with ASP 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ARG* 2.9 19.3 + - - +
192C LYS* 4.7 14.4 - - + +
193C TYR* 3.1 31.4 + - - -
350C PHE* 3.1 18.1 - - - +
351C LYS* 3.4 18.9 - - - +
353C PHE* 1.3 80.2 - - - +
355C ASP* 1.3 68.8 + - - +
356C VAL* 4.0 2.8 + - - +
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Residues in contact with ASP 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351C LYS 3.8 6.9 + - - +
352C ARG 3.3 3.2 + - - -
353C PHE 3.1 0.2 - - - -
354C ASP* 1.3 86.6 - - - +
356C VAL* 1.3 75.4 + - - +
357C GLU* 3.2 30.2 + - + +
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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