Contacts of the helix formed by residues 359 - 363 (chain B) in PDB entry 3V6R
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 ILE 359 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B SER 3.9 8.3 - - - +
170B LEU* 3.7 29.8 - - + -
171B TYR* 3.8 28.0 - - + -
174B LEU* 3.8 22.2 - - + -
335B LEU* 3.7 28.9 - - + -
353B ALA 3.5 22.9 - - - +
354B LEU* 4.1 7.9 - - - -
356B HIS* 3.0 2.6 + - + +
358B TYR* 1.3 88.0 - - + +
360B ASN* 1.3 57.8 + - - +
361B VAL 2.9 12.4 + - - -
362B TRP* 3.0 24.8 + - - +
363B TYR 4.1 1.4 + - - -
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Residues in contact with ASN 360 (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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102A GLN* 3.7 23.6 + - - +
386A THR* 5.9 3.6 - - - +
354B LEU 3.3 17.6 + - - +
355B GLN* 3.8 32.1 + - - +
356B HIS 2.7 21.9 + - - +
357B PRO* 4.2 4.7 + - + -
358B TYR 3.9 0.2 - - - -
359B ILE* 1.3 69.3 - - - +
361B VAL* 1.3 61.2 + - + +
362B TRP 3.1 0.4 - - - -
363B TYR* 3.0 41.4 + - - +
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Residues in contact with VAL 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASN* 5.5 0.7 - - - +
102A GLN* 3.4 38.9 + - + +
103A THR* 4.1 14.7 + - - +
384A GLU* 3.4 42.4 - - + +
164B GLU* 4.8 7.2 - - - +
167B SER* 4.7 2.5 - - - +
328B LYS* 4.3 2.0 - - - +
357B PRO 3.8 11.9 - - - +
358B TYR 4.0 11.0 - - - +
359B ILE 2.9 3.2 + - - +
360B ASN* 1.3 75.5 - - - +
362B TRP* 1.4 86.8 + - + +
363B TYR 5.2 0.6 - - - +
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Residues in contact with TRP 362 (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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101A ASN* 5.2 3.2 - - - +
103A THR* 4.4 24.2 - - + -
217A SER* 5.3 0.2 - - - -
219A MET* 3.3 43.7 - - + -
164B GLU* 3.5 41.5 - - + -
167B SER* 3.0 37.4 + - - -
168B TYR* 3.4 26.3 - + + +
171B TYR* 3.2 37.0 + - + -
359B ILE 3.0 10.1 + - - +
361B VAL* 1.4 91.0 - - + +
363B TYR* 1.3 65.7 + - - +
364B ASP* 3.2 5.5 + - - +
367B GLU* 4.0 1.2 - - - +
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Residues in contact with TYR 363 (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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100A GLN 4.5 0.2 - - - +
101A ASN* 3.5 20.6 - - - +
102A GLN 5.0 0.7 + - - -
387A ILE* 5.0 8.4 - - + +
171B TYR* 3.7 9.8 - + - -
351B ASP 5.7 0.4 - - - -
354B LEU* 3.7 23.6 - - + +
355B GLN* 3.9 16.6 + - - -
359B ILE 4.1 0.4 + - - -
360B ASN* 3.0 38.4 + - - +
361B VAL 3.5 0.4 - - - -
362B TRP* 1.3 76.2 - - - +
364B ASP* 1.3 59.4 + - - +
365B PRO* 3.9 22.0 - - + +
368B VAL* 3.3 35.7 - - + +
369B GLU* 2.7 29.8 + - - +
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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