Contacts of the helix formed by residues 47 - 54 (chain F) 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 ASP 47 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46F GLY* 1.3 72.6 - - - +
48F SER* 1.3 64.3 + - - +
49F MET* 2.7 44.9 + - - +
50F VAL* 3.0 14.1 + - - +
51F GLN* 3.0 11.6 + - - +
73F ILE 3.1 15.3 - - - +
76F ASP* 3.6 24.6 - - + +
101F TRP* 3.1 17.2 + - - +
102F VAL* 3.4 16.1 - - + +
103F GLY 3.6 8.0 + - - -
104F THR* 3.8 10.3 - - - +
105F ASN* 3.9 14.7 + - - +
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Residues in contact with SER 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F ASP* 1.3 75.0 - - - +
49F MET* 1.3 57.5 + - - +
51F GLN* 4.1 6.7 - - - -
52F LEU* 2.8 38.0 + - - +
73F ILE 3.4 2.8 + - - -
74F GLY* 3.2 13.8 - - - -
75F GLY 2.9 22.3 + - - -
105F ASN* 3.9 9.5 + - - -
196F HIS* 3.4 29.6 + - - -
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Residues in contact with MET 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F ASP* 2.7 27.2 + - - +
48F SER* 1.3 72.3 - - - +
50F VAL* 1.3 58.6 + - - +
53F MET* 3.7 1.0 + - - +
101F TRP* 3.6 38.6 - - + +
104F THR* 4.5 17.0 - - + -
140F LEU* 3.7 34.1 - - + +
195F LEU* 3.8 28.0 - - - +
196F HIS* 4.6 15.0 - - - -
197F LEU* 4.2 11.2 - - + -
202F TYR* 2.5 36.8 + - - -
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Residues in contact with VAL 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F PHE* 3.5 46.2 - - + +
45F VAL 3.6 6.5 - - - +
46F GLY* 3.5 23.1 - - - -
47F ASP 3.0 13.6 + - - +
49F MET* 1.3 74.1 - - - +
51F GLN* 1.3 66.3 + - - +
53F MET* 3.1 21.2 - - - +
70F ASN* 3.3 16.8 + - - +
72F GLY* 4.3 5.6 - - - -
99F VAL* 5.9 1.1 - - + -
101F TRP* 3.6 26.7 - - + +
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Residues in contact with GLN 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E PHE* 4.2 34.3 + - + +
193E ASP* 4.3 9.4 - - - +
27F GLN* 2.7 29.1 + - - +
30F ARG* 5.7 0.6 - - - +
31F PHE* 5.4 1.4 - - - -
47F ASP 3.0 7.7 + - - +
48F SER* 3.2 7.1 + - - +
50F VAL* 1.3 82.0 - - - +
52F LEU* 1.3 64.8 + - + +
53F MET 3.3 0.9 + - - -
54F GLN* 3.4 19.6 + - - +
55F GLN* 4.2 5.2 - - - +
70F ASN* 3.6 11.2 - - - +
72F GLY* 2.9 29.9 + - - +
73F ILE* 4.1 0.6 - - - +
74F GLY* 2.9 25.3 + - - -
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Residues in contact with LEU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E LEU* 5.2 14.4 - - + -
192E PHE* 4.0 30.5 - - + -
48F SER* 2.8 23.1 + - - +
51F GLN* 1.3 74.1 - - + +
53F MET* 1.3 65.9 + - - +
54F GLN 3.1 2.9 - - - -
55F GLN* 3.0 22.1 + - + +
56F TYR* 3.4 37.2 - - + +
192F PHE* 4.7 15.3 - - + -
196F HIS* 4.5 21.3 - - + -
197F LEU 4.7 3.4 - - - +
202F TYR* 3.4 13.5 - - + +
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Residues in contact with MET 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F PHE* 3.9 21.3 - - + -
49F MET 3.9 1.6 - - - +
50F VAL* 3.1 16.5 + - - +
52F LEU* 1.3 77.4 - - - +
54F GLN* 1.3 63.3 + - - +
55F GLN 3.2 0.9 + - - -
56F TYR* 3.3 15.4 + - - +
58F ILE* 4.9 3.0 - - + +
59F TRP* 3.4 26.4 + - + +
63F PHE* 3.5 25.4 - - + -
101F TRP* 4.6 7.9 - - + -
202F TYR* 3.5 36.5 + - + -
205F ILE* 4.5 10.5 - - + -
206F CYS* 3.1 31.2 - - - -
209F LEU* 4.5 7.4 - - + -
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Residues in contact with GLN 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ARG* 5.2 8.7 + - - +
50F VAL 4.0 0.6 + - - -
51F GLN 3.4 12.5 + - - +
52F LEU 3.1 0.6 - - - -
53F MET* 1.3 81.2 - - - +
55F GLN* 1.3 72.2 + - - +
56F TYR 3.2 1.9 + - - +
59F TRP* 3.8 47.6 - - + +
68F ALA 5.8 0.8 + - - -
70F ASN* 3.5 35.7 - - - +
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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