Contacts of the helix formed by residues 397 - 404 (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 GLY 397 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341B HIS* 3.6 9.4 - - - +
395B THR 3.5 1.6 + - - -
396B PRO* 1.3 72.5 - - - +
398B PRO* 1.4 77.1 - - - +
399B TYR 3.3 3.1 - - - -
400B GLU* 2.7 26.0 + - - +
401B ILE* 3.0 25.8 + - - +
532B ARG* 3.6 8.1 - - - -
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Residues in contact with PRO 398 (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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397B GLY* 1.4 81.8 - - - +
399B TYR* 1.4 52.3 + - - +
400B GLU* 4.8 0.2 - - - +
401B ILE* 3.3 10.6 + - + +
402B GLU* 2.9 36.0 + - - +
532B ARG* 3.6 18.8 - - - +
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Residues in contact with TYR 399 (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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34B HIS* 3.9 6.9 - - - -
344B ILE* 3.9 22.4 - - + -
348B ARG* 3.9 24.6 - - - +
379B PHE* 3.4 25.8 - + - -
383B GLU* 2.6 27.9 + - - +
386B MET* 3.6 13.3 - - + +
391B TYR* 3.0 34.3 - + - -
397B GLY 3.3 0.6 - - - -
398B PRO* 1.4 73.9 - - - +
400B GLU* 1.3 76.1 + - - +
402B GLU* 3.2 3.5 + - - -
403B HIS* 2.7 62.6 + + - -
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Residues in contact with GLU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B THR* 3.6 17.3 - - - +
340B SER* 2.8 31.0 + - - +
341B HIS* 3.2 10.4 + - - -
344B ILE* 4.5 7.2 - - + +
345B PRO* 6.0 0.2 - - - +
391B TYR* 3.5 35.0 - - + -
396B PRO* 4.3 9.0 - - + -
397B GLY* 2.7 38.1 + - - +
398B PRO* 4.8 0.2 - - - +
399B TYR* 1.3 86.1 - - - +
401B ILE* 1.4 57.6 + - - +
403B HIS 3.3 0.4 + - - +
404B THR* 2.7 38.4 + - - -
407B MET* 4.7 0.7 - - - -
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Residues in contact with ILE 401 (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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396B PRO* 3.3 23.6 - - + +
397B GLY 3.0 22.4 + - - +
398B PRO* 3.7 8.3 - - + +
400B GLU* 1.4 74.7 - - - +
402B GLU* 1.3 61.8 + - - +
404B THR 3.4 15.9 - - - +
407B MET* 3.9 24.2 - - + +
532B ARG* 4.0 8.7 - - - +
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Residues in contact with GLU 402 (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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33B LYS* 5.5 1.0 + - - -
398B PRO 2.9 17.6 + - - +
399B TYR* 3.7 1.6 - - - +
401B ILE* 1.3 76.4 - - - +
403B HIS* 1.3 76.5 + - + +
404B THR 4.8 0.7 - - - +
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Residues in contact with HIS 403 (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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33B LYS* 3.2 27.9 + - - +
34B HIS* 3.4 53.2 - + + +
383B GLU* 4.3 4.8 + - - -
391B TYR* 4.8 1.1 - - + +
399B TYR* 2.7 62.0 + + + +
400B GLU* 4.2 2.7 - - - +
402B GLU* 1.3 90.5 - - + +
404B THR* 1.3 57.6 + - - +
405B ASP 3.8 0.3 + - - -
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Residues in contact with THR 404 (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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33B LYS* 5.0 0.2 - - - -
34B HIS 4.2 5.6 - - - +
35B GLN* 3.8 12.0 + - + -
36B THR* 2.6 49.6 + - - +
391B TYR* 4.3 4.2 - - - -
400B GLU 2.7 18.2 + - - -
401B ILE 3.4 12.6 - - - +
402B GLU 4.8 1.0 - - - +
403B HIS* 1.3 76.4 - - - +
405B ASP* 1.4 65.3 + - - +
406B GLU 3.2 30.9 - - - +
407B MET* 4.4 9.6 - - + +
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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