Contacts of the helix formed by residues 330 - 345 (chain C) in PDB entry 1P4V
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 LYS 330 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C VAL* 3.6 6.5 - - - +
325C LEU* 4.7 0.2 - - - -
328C GLY 5.7 0.2 - - - +
329C GLY* 1.3 74.9 - - - -
331C ALA* 1.3 66.7 + - - +
332C LEU* 4.1 16.2 - - + +
333C ASP* 3.1 30.9 + - - +
334C ALA* 3.0 18.4 + - - +
372C GLU* 5.8 5.6 - - - +
393C ARG* 4.4 13.1 - - - +
459C ASP* 3.7 6.1 - - - +
461C GLN* 4.3 15.0 - - - +
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Residues in contact with ALA 331 (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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325C LEU* 4.2 1.8 - - - -
330C LYS* 1.3 72.0 - - - +
332C LEU* 1.3 62.7 + - - +
334C ALA* 3.1 8.2 + - - +
335C VAL* 2.9 28.1 + - - +
372C GLU* 5.8 0.2 - - - +
457C ALA* 3.7 14.8 - - + +
459C ASP* 2.8 30.3 + - + +
463C ASN* 3.4 18.6 - - + +
464C LEU 4.1 0.2 - - - -
465C SER* 3.6 20.0 - - - +
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Residues in contact with LEU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C LYS* 3.1 14.9 - - + +
331C ALA* 1.3 79.4 - - - +
333C ASP* 1.3 62.2 + - - +
335C VAL* 3.4 4.8 - - + +
336C GLU* 3.2 22.7 + - - +
369C ILE* 3.4 37.0 - - + -
370C MET 4.4 2.0 - - - +
371C ASP* 4.0 28.5 - - + +
372C GLU* 4.9 4.2 + - - +
393C ARG* 3.5 35.2 - - - +
396C MET* 3.9 18.6 - - + -
397C GLU* 4.1 2.5 - - - +
465C SER* 3.4 14.9 + - - +
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Residues in contact with ASP 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C VAL* 4.1 15.6 - - + +
330C LYS* 3.1 38.4 + - - +
332C LEU* 1.3 76.5 - - - +
334C ALA* 1.3 58.5 + - - +
336C GLU* 3.8 3.5 - - - +
337C LYS* 3.0 31.9 + - - +
393C ARG* 2.7 38.8 + - - +
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Residues in contact with ALA 334 (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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321C ALA* 3.5 23.1 - - + +
324C VAL* 3.8 14.0 - - + +
325C LEU* 3.5 42.2 - - + -
330C LYS 3.0 7.7 + - - +
331C ALA 3.1 7.6 + - - +
333C ASP* 1.3 77.5 - - - +
335C VAL* 1.3 57.1 + - - +
337C LYS* 3.8 0.5 - - - +
338C GLY 2.9 24.9 + - - -
457C ALA* 4.9 2.7 - - + -
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Residues in contact with VAL 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C ALA 2.9 14.4 + - - +
332C LEU* 3.4 15.5 - - - +
334C ALA* 1.3 73.3 - - - +
336C GLU* 1.3 69.5 + - - +
339C VAL* 3.0 29.3 + - - +
369C ILE* 4.6 4.5 - - + -
455C MET* 3.7 26.7 - - + +
457C ALA* 3.8 20.2 - - + +
465C SER* 3.7 19.7 - - - +
466C GLY* 3.8 15.7 - - - +
467C ALA* 3.8 23.3 - - + -
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Residues in contact with GLU 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C LEU 3.2 13.9 + - - +
333C ASP* 3.8 3.6 - - - +
335C VAL* 1.3 84.5 - - - +
337C LYS* 1.3 65.6 + - - +
339C VAL* 3.5 6.6 - - - +
340C ARG* 2.9 42.7 + - + +
369C ILE* 4.3 8.5 - - + -
389C ILE* 4.2 11.2 - - + -
390C SER* 2.7 33.2 + - - +
393C ARG* 2.7 43.5 + - - -
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Residues in contact with LYS 337 (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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320C GLU* 3.2 40.7 - - + +
323C LYS* 2.9 38.4 - - - +
324C VAL* 3.6 17.9 - - + +
333C ASP 3.0 18.0 + - - +
334C ALA 3.8 2.5 - - - +
336C GLU* 1.3 76.9 - - - +
338C GLY* 1.3 64.4 + - - +
340C ARG* 3.4 18.7 + - - +
341C LEU* 3.4 12.0 + - - +
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Residues in contact with GLY 338 (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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317C ALA* 3.5 32.1 - - - +
320C GLU* 4.2 4.0 - - - -
321C ALA 4.2 1.1 - - - -
334C ALA 2.9 17.4 + - - -
335C VAL 3.8 1.1 - - - -
336C GLU 3.2 0.2 - - - -
337C LYS* 1.3 79.4 - - - +
339C VAL* 1.3 61.1 + - - +
341C LEU* 3.4 16.8 - - - +
342C VAL 4.1 0.7 + - - -
455C MET* 3.8 12.6 - - - -
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Residues in contact with VAL 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C VAL 3.0 19.8 + - - +
336C GLU 3.5 5.4 - - - +
338C GLY* 1.3 72.4 - - - +
340C ARG* 1.3 68.6 + - - +
341C LEU 3.1 2.5 - - - -
342C VAL* 3.1 7.0 + - - +
343C GLU* 3.0 22.5 + - - +
389C ILE* 3.6 33.9 - - + -
453C ILE* 4.1 22.9 - - + +
455C MET* 3.7 26.2 - - + -
467C ALA* 4.0 14.4 - - + +
469C THR* 3.8 16.5 - - + +
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Residues in contact with ARG 340 (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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336C GLU* 2.9 34.1 + - - +
337C LYS* 3.6 10.1 - - - +
338C GLY 3.3 0.2 - - - -
339C VAL* 1.3 77.3 - - - +
341C LEU* 1.3 62.6 + - - +
343C GLU* 3.2 13.6 + - - +
344C ASP* 2.9 41.6 + - - +
387C ASN* 3.4 35.1 + - - +
389C ILE* 3.6 17.7 - - + -
390C SER* 2.8 36.7 + - - -
418C PHE* 4.8 3.8 - - - -
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Residues in contact with LEU 341 (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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316C HIS* 3.4 55.4 - - + +
317C ALA* 3.7 4.3 - - + -
320C GLU* 3.5 29.8 - - + +
337C LYS 3.4 5.1 + - - +
338C GLY 3.4 11.4 - - - +
340C ARG* 1.3 80.6 - - - +
342C VAL* 1.3 61.5 + - + +
344C ASP* 3.6 9.1 + - + +
345C ASP* 3.4 19.1 + - - +
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Residues in contact with VAL 342 (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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313C PHE* 4.3 20.2 - - + +
316C HIS* 5.1 4.9 - - - +
317C ALA* 4.1 14.6 - - + -
338C GLY 4.2 0.2 - - - +
339C VAL 3.1 8.2 + - - +
341C LEU* 1.3 79.3 - - + +
343C GLU* 1.3 67.2 + - - +
344C ASP 3.1 0.2 - - - -
345C ASP* 3.1 22.9 + - - +
348C GLU* 3.7 23.6 - - + +
351C VAL* 3.7 32.2 - - + +
453C ILE* 3.6 32.5 - - + -
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Residues in contact with GLU 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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339C VAL 3.0 13.6 + - - +
340C ARG* 3.2 8.1 + - - +
342C VAL* 1.3 78.0 - - - +
344C ASP* 1.3 61.5 + - - +
345C ASP 3.4 0.2 + - - -
351C VAL* 3.8 13.8 - - + +
352C GLY* 4.1 4.7 - - - -
353C TYR* 2.9 30.3 + - - +
386C LYS* 3.4 14.6 - - - +
387C ASN* 2.9 28.9 - - - +
388C PRO* 3.4 11.2 - - + +
389C ILE* 3.0 39.4 + - - +
469C THR* 2.7 29.8 + - + +
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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
----------------------------------------------------------
340C ARG* 2.9 30.7 + - - +
341C LEU* 3.8 9.6 - - + +
342C VAL 3.1 0.2 - - - -
343C GLU* 1.3 76.8 - - - +
345C ASP* 1.3 57.5 + - - +
346C PRO* 3.1 14.4 - - - +
353C TYR* 3.7 10.6 - - - -
386C LYS* 3.9 19.9 + - + +
387C ASN* 3.0 27.9 + - - +
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Residues in contact with ASP 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C HIS* 4.8 10.6 + - - +
341C LEU 3.4 11.0 + - - +
342C VAL* 3.1 15.2 + - - +
344C ASP* 1.3 76.8 - - - +
346C PRO* 1.3 70.1 - - - +
347C THR* 2.5 34.8 + - - +
348C GLU* 3.0 30.6 + - + +
353C TYR 3.1 11.4 - - - +
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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