Contacts of the helix formed by residues 45 - 57 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D CYS* 4.6 4.0 - - - -
43D MET 4.4 0.2 + - - -
44D PHE* 1.3 75.7 - - - +
46D LEU* 1.3 65.2 + - - +
47D GLU* 3.4 8.0 + - - +
48D GLU* 2.8 44.0 + - - +
49D ARG* 3.0 22.8 + - - +
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Residues in contact with LEU 46 (chain D).
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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34D VAL* 3.8 34.5 - - + +
35D THR 4.0 11.4 - - - -
36D GLU* 4.1 16.2 - - + +
45D THR* 1.3 73.8 - - - +
47D GLU* 1.3 60.3 + - + +
49D ARG* 3.4 29.4 + - - +
50D LYS* 3.0 26.9 + - - +
67D VAL* 3.9 16.4 - - + +
68D HIS 4.4 7.2 - - - +
69D HIS* 2.9 41.1 - - + +
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Residues in contact with GLU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D THR* 3.2 6.1 + - - +
46D LEU* 1.3 78.5 - - + +
48D GLU* 1.3 65.2 + - - +
50D LYS* 3.3 25.9 + - - +
51D LYS* 3.0 25.1 + - - +
67D VAL* 4.1 21.5 - - + +
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Residues in contact with GLU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D PHE* 3.1 29.3 - - + +
45D THR* 2.8 52.6 + - - +
47D GLU* 1.3 75.9 - - - +
49D ARG* 1.3 62.1 + - - +
51D LYS* 3.4 6.2 + - - +
52D LEU* 3.0 28.0 + - + +
155D LYS* 3.6 19.6 + - - -
158D GLU* 5.2 0.3 - - - +
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Residues in contact with ARG 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D SER* 2.9 28.7 + - - +
9D PHE 3.1 27.1 - - - +
10D ASP* 3.7 15.9 - - - +
11D PRO* 5.2 0.7 - - + -
34D VAL* 3.7 10.5 - - + +
35D THR 4.4 3.0 + - - -
36D GLU* 5.6 1.6 - - - +
37D ASN 5.9 0.4 - - - +
42D CYS* 3.2 24.3 - - - +
44D PHE* 3.0 39.4 + - + -
45D THR 3.0 9.3 + - - +
46D LEU* 3.4 48.2 - - - +
47D GLU 3.2 0.2 - - - -
48D GLU* 1.3 75.7 - - - +
50D LYS* 1.3 66.2 + - - +
52D LEU* 3.4 9.2 + - + +
53D ILE* 3.0 30.6 + - + +
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Residues in contact with LYS 50 (chain D).
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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34D VAL* 4.2 8.0 - - + +
46D LEU 3.0 17.1 + - - +
47D GLU* 3.3 25.7 + - - +
49D ARG* 1.3 75.9 - - - +
51D LYS* 1.3 56.9 + - - +
53D ILE* 3.2 3.5 + - - +
54D GLU* 2.9 61.2 + - - +
65D VAL* 3.7 32.5 + - + +
66D ASP* 4.2 8.4 + - - +
67D VAL* 3.6 26.5 - - + +
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Residues in contact with LYS 51 (chain D).
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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47D GLU* 3.0 17.1 + - - +
48D GLU* 3.6 7.0 - - - +
50D LYS* 1.3 78.0 - - - +
52D LEU* 1.3 62.7 + - - +
54D GLU* 3.3 14.7 + - - +
55D GLU* 3.0 34.0 + - + +
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Residues in contact with LEU 52 (chain D).
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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9D PHE 6.0 0.2 - - - +
11D PRO* 4.3 18.4 - - + -
12D ILE* 5.0 4.3 - - + -
44D PHE* 4.7 14.6 - - + -
48D GLU* 3.0 16.4 + - + +
49D ARG* 3.7 11.9 - - + +
51D LYS* 1.3 74.7 - - - +
53D ILE* 1.3 58.6 + - - +
55D GLU* 3.2 21.6 + - - +
56D VAL* 2.9 34.9 + - - +
147D GLU* 3.7 20.0 - - + +
148D VAL* 4.2 18.2 - - + -
151D ALA* 3.7 32.8 - - + -
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Residues in contact with ILE 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D PHE* 3.7 29.2 - - + +
12D ILE* 3.8 27.8 - - + -
32D VAL* 4.2 7.9 - - + -
34D VAL* 3.5 27.8 - - + -
49D ARG 3.0 20.7 + - - +
50D LYS 3.5 6.1 - - - +
52D LEU* 1.3 76.2 - - + +
54D GLU* 1.3 58.1 + - - +
56D VAL* 3.2 6.1 + - - -
57D LEU* 2.8 52.9 + - + +
65D VAL* 3.6 17.9 - - + -
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Residues in contact with GLU 54 (chain D).
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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50D LYS* 2.9 49.3 + - - +
51D LYS* 3.7 15.1 - - + +
53D ILE* 1.3 73.7 - - - +
55D GLU* 1.3 65.5 + - - +
57D LEU* 3.9 2.1 - - - -
58D SER* 3.2 24.6 + - - -
65D VAL* 3.8 27.8 + - + +
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Residues in contact with GLU 55 (chain D).
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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51D LYS* 3.0 22.7 + - + +
52D LEU* 3.4 29.3 + - - +
54D GLU* 1.3 77.9 - - - +
56D VAL* 1.3 62.9 + - - +
58D SER* 3.3 19.4 + - - -
147D GLU* 3.9 29.6 - - + +
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ILE* 4.2 6.3 - - + -
17D VAL* 4.0 21.2 - - + +
52D LEU 2.9 23.3 + - - +
53D ILE* 3.7 5.8 - - - +
55D GLU* 1.3 77.9 - - - +
57D LEU* 1.3 60.9 + - + +
58D SER* 3.4 3.1 + - - -
59D ASP* 5.0 3.8 - - - +
145D PRO* 3.6 33.7 - - + -
147D GLU* 3.9 33.1 - - + +
148D VAL* 4.2 8.5 - - + -
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Residues in contact with LEU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ILE* 4.8 1.6 - - + -
17D VAL* 4.4 18.8 - - + -
20D ILE* 4.2 20.6 - - + -
32D VAL* 4.2 9.6 - - + -
53D ILE* 2.8 41.8 + - + +
54D GLU* 3.9 3.1 - - - +
56D VAL* 1.3 80.4 - - + +
58D SER* 1.3 63.7 + - - +
59D ASP* 3.2 3.6 - - - -
60D LEU* 2.8 45.5 + - + +
63D VAL* 3.7 30.7 - - + +
65D VAL* 4.2 4.9 - - + -
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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