Contacts of the helix formed by residues 45 - 57 (chain F) in PDB entry 1VLH
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 THR 45 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42F CYS* 4.8 4.5 - - - -
44F PHE* 1.3 75.5 - - - +
46F LEU* 1.3 65.4 + - - +
47F GLU* 3.6 7.8 + - - +
48F GLU* 2.7 44.5 + - - +
49F ARG* 3.0 23.2 + - - +
155F LYS* 5.2 2.0 - - - +
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Residues in contact with LEU 46 (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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34F VAL* 3.4 37.2 - - + +
35F THR 4.1 9.4 - - - -
36F GLU* 4.2 16.8 - - + +
45F THR* 1.3 73.3 - - - +
47F GLU* 1.3 57.9 + - - +
49F ARG* 3.3 28.4 + - - +
50F LYS* 3.0 27.5 + - - +
67F VAL* 3.6 16.4 - - + +
68F HIS 4.2 11.9 - - - +
69F HIS* 3.2 37.5 - - + +
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Residues in contact with GLU 47 (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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45F THR* 3.1 6.5 + - - +
46F LEU* 1.3 76.7 - - - +
48F GLU* 1.3 65.7 + - - +
50F LYS* 3.3 29.5 + - + +
51F LYS* 3.0 53.0 + - + +
67F VAL* 5.2 7.4 - - + -
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Residues in contact with GLU 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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44F PHE* 3.1 18.4 - - + -
45F THR* 2.7 49.8 + - + +
47F GLU* 1.3 75.6 - - - +
49F ARG* 1.3 57.2 + - - +
51F LYS* 3.4 7.8 + - - +
52F LEU* 3.0 32.8 + - + +
155F LYS* 2.8 32.3 + - - +
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Residues in contact with ARG 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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8F SER* 2.8 51.2 + - - +
9F PHE* 3.1 18.6 - - + +
10F ASP* 3.5 13.9 + - - +
11F PRO* 5.2 0.7 - - + -
34F VAL* 3.8 10.1 - - + -
35F THR 4.4 2.4 + - - -
36F GLU* 5.6 2.0 - - - +
37F ASN 5.8 0.6 - - - +
42F CYS* 3.2 27.1 - - - +
44F PHE* 2.8 40.4 + - + -
45F THR 3.0 13.7 + - - +
46F LEU* 3.6 42.4 - - - +
48F GLU* 1.3 75.1 - - - +
50F LYS* 1.3 65.4 + - - +
52F LEU* 3.5 8.3 + - + +
53F ILE* 3.0 31.0 + - - +
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Residues in contact with LYS 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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34F VAL* 4.1 10.7 - - + +
46F LEU 3.0 15.2 + - - +
47F GLU* 3.4 27.1 - - - +
49F ARG* 1.3 76.4 - - - +
51F LYS* 1.3 56.1 + - - +
53F ILE* 3.4 2.8 + - - +
54F GLU* 3.0 61.9 + - - +
65F VAL* 3.8 25.5 + - + +
66F ASP* 3.9 16.0 + - - -
67F VAL* 3.9 25.9 - - + +
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Residues in contact with LYS 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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47F GLU* 3.0 45.1 + - + +
48F GLU* 3.8 7.4 - - - +
50F LYS* 1.3 72.5 - - - +
52F LEU* 1.3 65.7 + - - +
54F GLU* 3.3 14.5 + - - +
55F GLU* 3.0 35.7 + - - +
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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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9F PHE 6.1 0.2 - - - +
11F PRO* 4.4 18.2 - - + -
12F ILE* 5.1 2.2 - - + +
44F PHE* 4.7 13.7 - - + -
48F GLU 3.0 18.4 + - - +
49F ARG* 3.5 9.2 - - - +
51F LYS* 1.3 76.3 - - - +
53F ILE* 1.3 58.7 + - + +
55F GLU* 3.2 16.7 + - - +
56F VAL* 2.9 34.4 + - - +
147F GLU* 3.8 35.9 - - + +
148F VAL* 4.0 19.3 - - + -
151F ALA* 4.0 21.8 - - + -
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Residues in contact with ILE 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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9F PHE* 3.6 28.3 - - + +
12F ILE* 4.0 25.4 - - + -
32F VAL* 4.1 11.7 - - + -
34F VAL* 3.6 26.5 - - + -
49F ARG 3.0 18.7 + - - +
50F LYS 3.7 4.0 - - - +
51F LYS 3.3 0.2 - - - -
52F LEU* 1.3 75.9 - - + +
54F GLU* 1.3 57.3 + - - +
56F VAL* 3.2 5.7 + - - -
57F LEU* 2.8 55.4 + - + +
65F VAL* 3.6 16.6 - - + -
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Residues in contact with GLU 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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50F LYS* 3.0 51.5 + - - +
51F LYS* 3.7 16.4 - - - +
53F ILE* 1.3 73.0 - - - +
55F GLU* 1.3 65.7 + - - +
57F LEU* 3.9 1.5 - - - -
58F SER* 3.3 23.7 + - - -
65F VAL* 3.7 28.9 + - + +
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Residues in contact with GLU 55 (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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51F LYS* 3.0 29.8 + - + +
52F LEU* 3.4 17.8 - - - +
54F GLU* 1.3 74.4 - - - +
56F VAL* 1.3 63.3 + - - +
58F SER* 3.2 22.3 + - - -
147F GLU* 4.1 31.4 - - + +
150F ARG* 5.4 1.6 + - - -
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Residues in contact with VAL 56 (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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12F ILE* 4.2 6.3 - - + -
17F VAL* 3.7 25.1 - - + +
52F LEU 2.9 21.1 + - - +
53F ILE* 3.2 6.9 + - - +
55F GLU* 1.3 78.5 - - - +
57F LEU* 1.3 63.3 - - + +
58F SER* 3.2 4.9 + - - -
59F ASP* 5.6 1.2 - - - +
145F PRO* 3.7 36.6 - - + -
147F GLU* 3.8 28.0 - - + +
148F VAL* 4.1 9.4 - - + -
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Residues in contact with LEU 57 (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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12F ILE* 4.8 0.4 - - + -
17F VAL* 4.4 13.9 - - + -
20F ILE* 4.1 19.7 - - + -
32F VAL* 4.0 22.4 - - + -
53F ILE* 2.8 43.1 + - + +
54F GLU* 3.9 3.4 - - - +
56F VAL* 1.3 86.2 - - + +
58F SER* 1.3 63.7 + - - +
59F ASP* 3.3 2.9 - - - -
60F LEU* 2.9 47.0 + - + +
63F VAL* 4.1 15.4 - - + +
65F VAL* 4.1 6.5 - - + -
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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