Contacts of the helix formed by residues 368 - 374 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A ILE* 3.9 19.5 - - + +
266A GLU* 3.4 32.5 - - - +
267A LEU* 3.7 27.4 - - + +
270A GLN* 4.0 9.0 - - + -
286A LEU* 4.0 17.0 - - + +
290A THR* 3.8 27.8 - - + +
309A TYR* 4.3 10.7 - - + -
362A VAL* 3.6 3.5 - - - +
367A ARG* 1.3 77.4 - - - +
369A PRO* 1.4 74.5 - - + +
370A SER* 3.9 6.1 - - - +
371A ALA* 3.0 20.6 + - + +
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Residues in contact with PRO 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A GLU* 3.6 12.8 - - + +
270A GLN* 3.5 39.7 - - + +
311A ARG* 5.5 0.2 - - - -
359A GLN* 5.9 0.4 - - - +
362A VAL* 4.0 17.9 - - + -
368A LEU* 1.4 90.9 - - + +
370A SER* 1.4 57.4 + - - +
371A ALA 3.1 2.8 + - - -
372A LEU* 3.4 27.4 + - + +
373A ASP* 4.5 1.7 + - - -
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Residues in contact with SER 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLU* 2.7 34.2 + - - -
308A ASN 3.8 11.4 + - - +
309A TYR* 5.5 2.8 - - - -
311A ARG* 3.4 25.5 + - - +
312A HIS* 3.3 26.2 + - - -
368A LEU* 3.9 6.9 - - - +
369A PRO* 1.4 72.1 - - - +
371A ALA* 1.4 62.9 + - - +
372A LEU 3.2 1.6 - - - -
373A ASP* 3.2 22.8 + - - +
374A ASN* 4.1 1.4 + - - +
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Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ASN* 3.6 35.3 + - + +
358A LYS* 3.2 18.1 - - + +
362A VAL* 4.8 2.5 - - + -
367A ARG* 3.8 18.4 - - + -
368A LEU* 3.0 16.4 + - - +
370A SER* 1.4 77.7 + - - +
372A LEU* 1.4 62.1 + - - +
374A ASN* 3.1 25.8 + - - +
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Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A GLN* 3.1 66.2 + - + +
358A LYS* 3.8 16.8 - - + +
359A GLN* 3.5 35.7 - - + +
362A VAL* 4.0 15.0 - - + -
369A PRO* 3.4 24.0 - - + +
370A SER 3.2 0.2 - - - -
371A ALA* 1.4 77.4 - - - +
373A ASP* 1.4 60.3 + - - +
374A ASN 3.2 0.9 + - - -
375A ARG* 3.4 14.0 - - - +
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Residues in contact with ASP 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A SER* 5.0 2.8 + - - -
311A ARG* 2.8 48.8 + - + +
318A PRO* 3.5 2.1 - - - +
319A GLY* 3.2 39.7 + - - +
320A SER 4.4 9.2 - - - +
322A PRO* 4.3 10.2 - - - +
369A PRO 5.5 1.1 - - - -
370A SER* 3.2 16.5 + - - +
371A ALA 3.2 1.2 - - - -
372A LEU* 1.4 76.2 - - - +
374A ASN* 1.3 58.2 + - - +
375A ARG* 3.5 16.0 + - - +
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Residues in contact with ASN 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLY* 6.0 4.2 - - - -
307A GLU* 3.1 47.1 + - - +
308A ASN* 4.3 12.2 + - - +
310A SER* 3.4 20.2 + - - +
322A PRO* 5.8 0.4 - - - -
354A ASP* 4.6 0.2 - - - +
358A LYS* 3.1 27.4 + - - -
370A SER 4.1 0.8 + - - +
371A ALA 3.1 13.4 + - - +
373A ASP* 1.3 73.7 - - - +
375A ARG* 1.4 57.8 + - - +
7D T 6.3 0.4 - - - +
8D T 4.9 6.1 + - - -
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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