Contacts of the helix formed by residues 368 - 374 (chain B) in PDB entry 3V4R
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 LEU 368 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263B ILE* 3.9 18.6 - - + +
266B GLU* 3.4 33.4 - - - +
267B LEU* 3.7 28.0 - - + +
270B GLN* 4.0 8.5 - - + -
286B LEU* 4.0 17.9 - - + +
290B THR* 3.8 27.1 - - + +
309B TYR* 4.3 10.7 - - + -
362B VAL* 3.6 4.1 - - - +
367B ARG* 1.3 76.1 - - - +
369B PRO* 1.4 73.7 - - + +
370B SER* 3.0 7.8 + - - +
371B ALA* 3.0 18.4 + - + +
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Residues in contact with PRO 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B GLU* 3.6 16.4 - - + +
270B GLN* 3.4 39.9 - - + +
311B ARG* 5.4 0.4 - - - -
359B GLN* 5.9 0.2 - - - +
362B VAL* 4.0 19.3 - - + -
368B LEU* 1.4 85.8 - - + +
370B SER* 1.4 54.9 + - - +
371B ALA 3.1 5.5 + - - -
372B LEU* 3.4 27.1 + - + +
373B ASP* 4.5 1.7 + - - -
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Residues in contact with SER 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B GLU* 2.7 34.2 + - - -
308B ASN 3.8 10.8 + - - +
309B TYR* 5.5 2.6 - - - -
311B ARG* 3.4 31.3 + - - +
312B HIS* 3.3 21.9 + - - -
368B LEU* 3.9 7.1 - - - +
369B PRO* 1.4 73.6 - - - +
371B ALA* 1.4 61.8 + - - +
372B LEU 3.2 0.4 - - - -
373B ASP* 3.2 22.8 + - - +
374B ASN 4.1 1.7 + - - -
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Residues in contact with ALA 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B ASN* 3.6 34.2 + - + +
358B LYS* 3.2 17.7 - - + +
362B VAL* 4.8 3.1 - - + -
367B ARG* 3.8 18.8 - - + -
368B LEU* 3.0 16.1 + - + +
370B SER* 1.4 78.6 + - - +
372B LEU* 1.4 62.5 + - - +
374B ASN* 3.2 24.8 + - - +
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B GLN* 3.1 68.1 + - - +
358B LYS* 3.8 17.0 - - + -
359B GLN* 3.5 35.7 - - + +
362B VAL* 4.0 15.0 - - + -
369B PRO* 3.4 24.0 - - + +
370B SER 3.2 0.6 - - - -
371B ALA* 1.4 77.3 - - - +
373B ASP* 1.4 61.4 + - - +
374B ASN 3.2 1.1 + - - -
375B ARG* 3.4 14.4 - - - +
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Residues in contact with ASP 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B SER* 5.0 2.9 + - - -
311B ARG* 2.8 49.7 + - + +
318B PRO* 3.5 1.6 - - - +
319B GLY* 3.2 39.8 + - - +
320B SER 4.4 9.1 - - - +
322B PRO* 4.2 10.7 - - - +
369B PRO 5.4 0.9 - - - -
370B SER* 3.2 17.5 + - - +
371B ALA 3.2 1.6 - - - -
372B LEU* 1.4 77.1 - - - +
374B ASN* 1.3 54.8 + - - +
375B ARG* 3.5 16.2 + - - +
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Residues in contact with ASN 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B GLY* 5.7 6.5 - - - -
307B GLU* 3.1 45.2 + - - +
308B ASN* 4.3 12.3 + - - +
310B SER* 3.4 20.1 + - - +
311B ARG 5.6 0.2 - - - +
322B PRO* 5.7 0.7 - - - -
358B LYS* 3.1 27.5 + - - -
370B SER 4.1 1.0 + - - -
371B ALA 3.2 13.2 + - - +
373B ASP* 1.3 73.6 - - - +
375B ARG* 1.4 59.0 + - - +
7C T 5.4 7.8 + - - +
8C T 5.8 1.4 + - - -
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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