Contacts of the helix formed by residues 336 - 348 (chain D) in PDB entry 6V3O
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 ASN 336 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335D CYS* 1.3 79.2 - - - +
337D ASP* 1.3 60.8 + - - +
338D GLU* 3.7 14.3 + - - +
339D LEU 3.7 13.9 - - - +
340D ARG* 3.0 28.0 + - - +
418D LEU* 4.8 2.8 + - - +
421D LYS* 3.9 12.7 - - - +
422D SER* 2.9 39.0 + - - +
425D ASP* 2.8 39.7 + - - +
426D CYS* 4.0 1.8 - - - -
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Residues in contact with ASP 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335D CYS 4.9 1.2 - - - +
336D ASN* 1.3 75.9 + - - +
338D GLU* 1.3 63.9 + - - +
340D ARG* 3.2 13.5 + - - +
341D VAL* 3.2 32.0 + - + +
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Residues in contact with GLU 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D ASN* 3.3 13.4 + - + +
337D ASP* 1.3 79.9 - - - +
339D LEU* 1.3 62.4 + - - +
341D VAL* 3.8 8.5 + - + +
342D ARG* 3.3 26.4 + - + +
418D LEU* 3.5 29.2 - - + +
421D LYS* 5.0 9.4 + - - +
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Residues in contact with LEU 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335D CYS* 4.2 2.5 - - + -
336D ASN* 3.7 19.3 - - + +
337D ASP 3.4 0.2 - - - -
338D GLU* 1.3 79.1 - - - +
340D ARG* 1.3 57.8 + - - +
342D ARG* 3.1 3.3 + - - +
343D ALA* 2.8 28.5 + - + +
370D PRO* 3.5 33.9 - - + +
371D TYR* 3.5 20.4 - - + -
374D ILE* 3.6 32.1 - - + -
418D LEU* 4.1 18.0 - - + +
419D CYS* 4.0 8.3 - - - +
422D SER* 3.4 28.5 - - - +
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Residues in contact with ARG 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D TRP* 4.3 18.0 + - - -
334D ARG* 5.0 2.0 - - - +
335D CYS* 3.7 39.6 + - - +
336D ASN 3.0 21.2 + - - +
337D ASP* 3.2 14.1 + - - +
339D LEU* 1.3 77.9 - - - +
341D VAL* 1.3 61.9 + - + +
343D ALA* 3.2 7.1 + - + +
344D GLU* 3.0 29.0 + - + +
370D PRO* 5.4 1.7 - - + +
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Residues in contact with VAL 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D ASP* 3.2 15.2 + - + +
338D GLU* 3.8 12.3 - - + +
340D ARG* 1.3 78.4 - - + +
342D ARG* 1.3 65.3 + - + +
344D GLU* 4.4 4.7 - - - +
345D GLU* 2.9 29.6 + - - +
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Residues in contact with ARG 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D GLU* 3.3 17.4 + - + +
339D LEU 3.1 9.3 + - - +
341D VAL* 1.3 83.0 - - + +
343D ALA* 1.3 66.1 + - - +
345D GLU* 2.9 33.0 + - - +
346D LEU* 3.1 60.0 + - - +
374D ILE* 4.9 6.6 - - + +
377D HIS* 4.5 11.3 + - - -
415D PRO* 6.0 4.8 - - - +
418D LEU* 4.1 23.1 - - + +
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Residues in contact with ALA 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D LEU* 2.8 20.8 + - + +
340D ARG* 3.2 6.3 + - + +
342D ARG* 1.3 74.0 - - - +
344D GLU* 1.3 60.0 + - - +
346D LEU* 3.2 9.5 + - - -
347D HIS* 3.3 18.5 + - + +
370D PRO* 4.1 35.2 - - + +
373D VAL* 3.6 19.9 - - + +
374D ILE* 4.3 6.7 - - + +
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Residues in contact with GLU 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340D ARG* 3.0 18.8 + - + +
341D VAL* 4.4 4.5 - - - +
343D ALA* 1.3 73.5 - - - +
345D GLU* 1.3 67.2 + - - +
347D HIS* 3.2 33.0 + - + +
348D SER* 3.8 7.7 + - - +
367D PRO* 5.7 2.4 - - - +
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Residues in contact with GLU 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D VAL 2.9 21.1 + - - +
342D ARG* 2.9 35.7 + - - +
344D GLU* 1.3 77.4 - - - +
346D LEU* 1.3 61.2 + - - +
348D SER* 3.2 26.5 + - - +
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Residues in contact with LEU 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D ARG* 3.1 45.7 + - - +
343D ALA 3.6 7.0 - - - +
344D GLU 3.2 0.2 - - - -
345D GLU* 1.3 73.7 - - - +
347D HIS* 1.3 60.0 + - - +
348D SER 3.3 0.4 - - - -
349D SER* 2.5 31.4 + - - +
373D VAL* 4.1 12.7 - - + +
374D ILE* 4.1 25.4 - - + -
377D HIS* 3.8 49.8 - - + +
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Residues in contact with HIS 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D ALA* 3.3 20.6 + - + -
344D GLU* 3.2 29.4 + - + +
345D GLU 3.2 1.2 - - - -
346D LEU* 1.3 79.1 - - - +
348D SER* 1.3 57.6 + - - +
349D SER* 2.9 12.5 + - - +
365D ILE 4.8 5.0 + - - -
366D PRO 4.7 0.8 - - - -
367D PRO* 3.1 51.1 - - + +
373D VAL* 4.2 17.8 - - + +
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Residues in contact with SER 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D GLU* 3.9 8.8 + - - +
345D GLU* 3.2 16.8 + - - +
347D HIS* 1.3 72.8 - - - +
349D SER* 1.3 60.2 + - - +
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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