Contacts of the helix formed by residues 342 - 353 (chain C) in PDB entry 1XV9
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 VAL 342 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264C PRO* 5.9 1.6 - - + -
265C VAL* 5.3 2.9 - - + -
268C ILE* 5.0 10.5 - - + -
337C ALA* 3.1 24.6 + - + +
340C ALA* 4.5 10.1 - - + +
341C GLY* 1.3 85.2 - - - +
343C GLY* 1.3 62.5 + - - +
344C ALA 3.8 0.4 - - - -
345C ILE* 2.9 29.0 - - + +
346C PHE* 3.2 11.3 + - - +
435C HIS* 3.6 22.7 - - + -
439C PHE* 4.0 21.1 - - + -
1002C F15 4.1 20.6 - - + -
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Residues in contact with GLY 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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256A LEU* 3.8 7.2 - - - +
339A SER 5.2 0.6 + - - -
337C ALA 3.6 2.8 + - - -
338C HIS* 3.3 43.5 + - - +
341C GLY 3.7 1.0 - - - -
342C VAL* 1.3 75.2 - - - +
344C ALA* 1.3 64.3 - - - +
345C ILE 3.0 1.7 + - - -
346C PHE* 3.0 13.8 + - - +
347C ASP* 3.1 14.2 + - - +
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Residues in contact with ALA 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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256A LEU* 3.7 34.1 - - + +
338C HIS* 5.3 0.2 - - - -
342C VAL 3.8 0.4 - - - -
343C GLY* 1.3 71.5 - - - +
345C ILE* 1.3 59.1 + - - +
347C ASP* 3.7 11.2 - - - +
348C ARG* 3.4 19.1 + - - +
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Residues in contact with ILE 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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342C VAL* 2.9 35.7 - - + +
344C ALA* 1.3 74.1 - - - +
346C PHE* 1.3 58.6 + - - +
347C ASP 3.2 1.6 - - - -
348C ARG* 2.8 15.3 + - + +
349C VAL* 2.7 35.1 + - + +
428C ILE* 4.2 18.6 - - + +
431C LYS* 4.0 24.0 - - + -
432C CYS* 3.6 24.7 - - - -
435C HIS* 3.8 23.5 - - + +
1002C F15 3.6 31.2 - - + -
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Residues in contact with PHE 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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322C ASP 3.6 8.7 - - - -
323C GLY* 3.8 9.9 - - - -
324C ILE* 3.4 18.8 - - + -
332C VAL* 3.4 17.7 - - + -
333C HIS 3.7 4.3 - - - -
334C ARG* 3.3 41.7 - - + -
337C ALA* 3.4 19.5 - - + -
338C HIS* 4.6 0.2 - + - -
342C VAL 3.2 11.2 - - - +
343C GLY 3.2 9.4 - - - +
345C ILE* 1.3 79.4 - - - +
347C ASP* 1.3 77.8 + - - +
349C VAL* 3.0 4.7 + - - +
350C LEU* 2.9 42.1 + - + +
1002C F15 3.7 30.5 - - + -
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Residues in contact with ASP 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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256A LEU* 5.7 0.5 - - - +
334C ARG* 3.9 21.9 + - - +
338C HIS* 2.8 41.6 + - - -
343C GLY 3.1 4.2 + - - -
344C ALA* 3.7 13.0 - - - +
346C PHE* 1.3 84.9 - - - +
348C ARG* 1.3 54.5 + - - +
350C LEU* 2.9 1.2 + - - +
351C THR* 2.6 43.0 + - + +
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Residues in contact with ARG 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 ALA 3.4 11.7 + - - +
345C ILE* 2.8 21.3 + - + +
347C ASP* 1.3 75.2 - - - +
349C VAL* 1.3 56.5 + - - +
351C THR* 3.6 8.0 - - - +
352C GLU* 2.9 46.2 + - + +
427C SER* 3.4 31.2 + - - -
428C ILE* 3.4 30.0 - - + +
431C LYS* 4.4 15.1 - - - +
271D ASP* 2.8 49.4 + - - +
272D ARG* 4.8 2.2 - - - +
273D PRO* 4.2 19.3 - - - +
320D ARG* 4.6 1.2 - - - +
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Residues in contact with VAL 349 (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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310C ILE* 4.9 3.4 - - + -
313C PHE* 3.8 20.9 - - + -
314C SER* 3.4 21.8 - - - +
324C ILE* 4.1 13.9 - - + -
345C ILE* 2.7 31.2 + - + +
346C PHE* 3.6 7.4 - - - +
348C ARG* 1.3 72.2 - - - +
350C LEU* 1.3 59.8 + - - +
353C LEU* 2.8 30.8 + - + +
354C VAL* 2.9 10.4 + - + -
428C ILE* 4.1 25.8 - - + -
432C CYS* 4.8 4.7 - - - -
1002C F15 4.3 11.9 - - + -
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Residues in contact with LEU 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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322C ASP* 3.6 25.8 - - - +
323C GLY 3.4 12.8 - - - +
324C ILE* 3.1 37.7 - - + -
334C ARG* 3.4 23.1 - - - +
346C PHE* 2.9 35.0 + - + +
347C ASP 2.9 5.3 + - - +
349C VAL* 1.3 81.1 - - - +
351C THR* 1.3 65.5 + - - +
352C GLU 3.0 0.5 + - - -
354C VAL* 3.0 22.0 + - + -
355C SER* 2.8 24.5 + - - -
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Residues in contact with THR 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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334C ARG* 4.5 5.7 - - - +
347C ASP* 2.6 44.9 + - + +
348C ARG* 3.6 7.4 - - + -
350C LEU* 1.3 74.0 - - - +
352C GLU* 1.3 75.1 + - + +
355C SER* 3.5 20.5 + - - -
356C LYS* 4.0 10.0 - - - +
278D ARG* 3.7 19.3 + - - -
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Residues in contact with GLU 352 (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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348C ARG* 2.9 39.6 + - + +
351C THR* 1.3 79.2 + - + +
353C LEU* 1.3 63.1 + - + +
356C LYS* 3.4 10.6 - - - +
421C ARG* 3.3 34.8 + - - -
424C ALA* 4.8 4.7 - - + +
428C ILE* 3.9 11.7 - - + -
270D PRO* 4.4 2.8 - - - +
271D ASP* 3.3 39.0 + - + +
278D ARG* 2.9 43.3 + - - -
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Residues in contact with LEU 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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310C ILE* 3.7 25.8 - - + +
311C ALA* 6.0 0.4 - - - -
314C SER* 3.2 25.6 - - - +
349C VAL* 2.8 23.8 + - + +
352C GLU* 1.3 86.7 - - + +
354C VAL* 1.3 55.7 + - - +
355C SER 3.4 0.9 - - - -
356C LYS* 3.4 1.6 + - - +
357C MET* 2.9 42.5 + - + +
421C ARG* 5.0 13.0 - - + +
424C ALA* 4.8 4.0 - - + -
425C LEU* 4.3 28.0 - - + +
428C ILE* 4.0 25.6 - - + -
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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