Contacts of the helix formed by residues 56 - 63 (chain E) in PDB entry 1VYH
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 TYR 56 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52E LEU* 3.5 30.8 - - + +
53E MET* 3.8 6.7 - - - +
54E GLN 3.1 2.7 - - - +
55E GLN* 1.3 85.4 - - + +
57E GLU* 1.3 67.9 + - - +
58E ILE* 3.0 16.2 - - + -
59E TRP* 2.9 20.4 + - - +
60E ARG* 4.1 1.4 + - - +
192E PHE* 3.7 2.1 - - - -
197E LEU 3.1 14.3 + - - -
198E THR* 3.5 2.3 - - - -
199E GLY* 3.4 28.0 - - - -
202E TYR* 3.5 38.1 - + + -
55F GLN* 3.1 51.2 - - + +
56F TYR* 6.1 3.4 - + - -
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Residues in contact with GLU 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E GLN 4.3 0.4 + - - -
56E TYR* 1.3 74.9 - - - +
58E ILE* 1.3 61.2 + - - +
59E TRP 3.3 0.7 + - - -
60E ARG* 3.4 51.4 + - - +
61E GLU* 3.4 19.1 + - - +
57F GLU* 5.4 14.6 - - + -
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Residues in contact with ILE 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E MET* 5.2 3.1 - - + +
56E TYR* 3.9 18.4 - - + -
57E GLU* 1.3 76.9 - - - +
59E TRP* 1.3 64.5 + - - +
61E GLU* 3.3 13.5 + - - +
62E LEU* 3.2 41.6 + - + +
63E PHE* 4.9 1.1 - - + -
199E GLY* 4.8 8.3 - - - +
202E TYR* 4.4 15.9 - - + -
203E ALA* 3.9 21.1 - - + -
206E CYS* 3.3 36.6 - - + -
207E LYS 4.9 1.6 - - - +
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Residues in contact with TRP 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E PHE* 3.7 47.3 - + - -
53E MET* 3.3 41.7 + - + +
54E GLN* 3.7 38.7 - - + +
56E TYR 2.9 9.0 + - - +
58E ILE* 1.3 76.8 - - - +
60E ARG* 1.3 60.1 + - + +
61E GLU 3.0 5.6 + - - -
63E PHE* 3.1 26.9 + + + -
64E SER* 3.0 43.7 + - - +
68E ALA* 4.1 27.1 + - + -
69E LEU 4.5 0.4 - - - -
70E ASN* 3.8 34.3 - - + -
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Residues in contact with ARG 60 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56E TYR 4.1 1.2 + - - -
57E GLU* 3.4 44.0 + - - +
59E TRP* 1.3 80.7 - - + +
61E GLU* 1.3 58.3 + - - +
62E LEU 3.6 0.2 - - - -
64E SER* 3.2 28.0 - - - +
65E PRO* 4.2 3.6 - - - +
380G GLU* 3.3 37.0 + - - +
381G HIS* 5.3 12.1 - - + +
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Residues in contact with GLU 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E GLU* 3.4 17.8 + - - +
58E ILE* 3.5 18.1 - - - +
59E TRP 3.0 0.2 - - - -
60E ARG* 1.3 82.1 - - - +
62E LEU* 1.3 77.9 + - + +
65E PRO* 4.3 9.8 - - - +
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Residues in contact with LEU 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E ILE* 3.2 35.4 + - + +
60E ARG 3.6 0.2 - - - -
61E GLU* 1.3 113.0 - - + +
63E PHE* 1.3 72.2 + - + +
65E PRO* 3.6 11.8 - - - +
66E LEU* 3.5 18.0 - - - +
206E CYS* 4.5 10.5 - - + +
207E LYS* 4.7 4.7 - - + +
210E HIS* 3.6 44.9 + - + +
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Residues in contact with PHE 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E VAL* 6.0 0.4 - - + -
44E PHE* 3.6 19.1 - + + -
53E MET* 4.0 8.7 - - - -
58E ILE* 4.7 2.2 - - + -
59E TRP* 3.1 41.3 + + + +
62E LEU* 1.3 87.1 - - + +
64E SER* 1.3 68.6 - - - +
65E PRO* 3.3 2.2 - - - -
66E LEU* 3.0 26.6 + - + +
67E HIS 3.7 0.2 + - - -
68E ALA* 3.4 26.6 - - + +
206E CYS* 3.9 37.5 - - + -
209E LEU* 4.6 4.9 - - + -
210E HIS* 3.9 27.1 - - + -
213E ILE* 3.7 24.7 - - + -
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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