Contacts of the helix formed by residues 397 - 404 (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 GLY 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A HIS* 3.6 11.0 - - - +
395A THR 3.6 1.2 + - - -
396A PRO* 1.3 72.2 - - - +
398A PRO* 1.4 75.6 - - - +
400A GLU* 2.7 28.5 + - - +
401A ILE* 3.0 23.3 + - - +
532A ARG* 3.5 9.0 - - - -
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Residues in contact with PRO 398 (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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348A ARG* 6.0 4.0 - - - +
397A GLY* 1.4 82.4 - - - +
399A TYR* 1.4 56.4 + - - +
400A GLU* 4.8 0.2 - - - +
401A ILE* 3.3 8.3 + - + +
402A GLU* 2.9 33.1 + - - +
532A ARG* 3.4 23.8 - - - +
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Residues in contact with TYR 399 (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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34A HIS* 3.9 4.2 - - - -
344A ILE* 3.9 23.3 - - + -
348A ARG* 4.7 12.9 - - - +
379A PHE* 3.4 30.7 - + - -
383A GLU* 2.6 27.9 + - - +
386A MET* 3.5 12.8 - - + +
391A TYR* 3.1 34.8 - + - -
397A GLY 3.3 0.4 - - - -
398A PRO* 1.4 74.6 - - - +
400A GLU* 1.3 74.6 + - - +
402A GLU* 3.2 3.4 + - - -
403A HIS* 2.7 65.8 + + - -
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Residues in contact with GLU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A THR* 3.7 16.4 - - - +
340A SER* 2.8 25.5 + - - +
341A HIS* 3.2 9.7 + - - -
344A ILE* 4.4 7.3 - - + +
391A TYR* 3.5 40.2 - - + -
396A PRO* 4.3 9.2 - - + -
397A GLY* 2.7 37.6 + - - +
398A PRO* 4.8 0.2 - - - +
399A TYR* 1.3 85.3 - - - +
401A ILE* 1.4 56.4 + - - +
403A HIS* 3.3 0.6 + - - -
404A THR* 2.7 37.5 + - - -
407A MET* 4.6 0.9 - - - -
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Residues in contact with ILE 401 (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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396A PRO* 3.3 23.8 - - + +
397A GLY 3.0 21.7 + - - +
398A PRO* 3.7 7.2 - - + +
400A GLU* 1.4 75.1 - - - +
402A GLU* 1.3 64.0 + - - +
404A THR 3.4 16.1 - - - +
407A MET* 3.9 23.5 - - + +
532A ARG* 3.6 14.6 - - - +
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Residues in contact with GLU 402 (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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398A PRO 2.9 18.0 + - - +
399A TYR* 3.2 6.3 + - - +
401A ILE* 1.3 79.2 - - - +
403A HIS* 1.3 73.5 + - + +
404A THR 4.8 1.1 - - - +
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Residues in contact with HIS 403 (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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34A HIS* 3.2 61.7 - + + +
383A GLU* 4.2 5.0 + - - -
391A TYR* 4.8 1.3 - - + +
399A TYR* 2.7 62.2 + + + +
400A GLU* 4.2 2.5 - - - +
402A GLU* 1.3 92.1 - - + +
404A THR* 1.3 60.5 + - - +
405A ASP 3.8 1.9 + - - -
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Residues in contact with THR 404 (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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34A HIS 4.4 5.4 - - - +
35A GLN* 3.8 11.6 + - + -
36A THR* 2.6 50.2 + - - +
391A TYR* 4.2 4.9 - - - -
400A GLU 2.7 16.5 + - - -
401A ILE 3.4 12.8 - - - +
402A GLU 4.8 1.3 - - - +
403A HIS* 1.3 76.4 - - - +
405A ASP* 1.4 64.1 + - - +
406A GLU 3.2 30.7 - - - +
407A MET* 4.4 9.3 - - + +
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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