Contacts of the helix formed by residues 46 - 60 (chain D) in PDB entry 1VLP
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 ASN 46 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D PHE* 1.3 75.1 - - - +
47D LYS* 1.3 65.3 + - - +
48D GLU* 3.5 11.3 + - - +
49D ALA* 2.9 32.9 + - - +
50D ILE* 3.1 28.7 + - - +
113D THR 4.3 12.1 - - - +
114D HIS* 5.8 3.4 - - + +
115D TYR* 4.3 1.3 - - - -
146D PHE* 3.1 28.9 + - - +
147D VAL* 3.9 11.3 - - + +
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Residues in contact with LYS 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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46D ASN* 1.3 75.6 - - - +
48D GLU* 1.3 58.0 + - + +
50D ILE* 3.3 9.5 + - + +
51D ASN* 2.9 31.4 + - - +
113D THR 5.0 0.4 + - - -
115D TYR* 3.3 38.7 + - + -
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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
----------------------------------------------------------
46D ASN* 3.3 11.1 + - - +
47D LYS* 1.3 77.4 - - + +
49D ALA* 1.3 63.1 + - - +
51D ASN* 3.4 7.0 + - - +
52D TRP* 3.1 24.1 + - - +
146D PHE* 3.8 25.8 - - + -
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Residues in contact with ALA 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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45D PHE* 4.0 24.9 - - + -
46D ASN* 2.9 24.9 + - - +
48D GLU* 1.3 75.6 - - - +
50D ILE* 1.3 57.5 + - - +
52D TRP* 3.4 2.8 + - - +
53D LEU* 3.0 34.3 + - - +
142D ALA* 4.3 9.2 - - + +
146D PHE* 3.7 25.5 - - + -
147D VAL* 4.4 2.7 - - + -
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Residues in contact with ILE 50 (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 PHE* 4.3 3.1 - - + -
46D ASN 3.1 17.5 + - - +
47D LYS* 3.7 7.9 - - + +
48D GLU 3.3 0.2 - - - -
49D ALA* 1.3 74.1 - - - +
51D ASN* 1.3 60.7 + - - +
53D LEU* 3.2 8.5 + - - +
54D LYS* 2.9 51.2 + - - +
103D PHE* 3.9 10.0 - - + -
105D SER* 3.6 25.1 - - - +
115D TYR* 3.6 38.4 - - + -
117D LEU* 3.6 23.8 - - + -
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Residues in contact with ASN 51 (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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47D LYS 2.9 17.1 + - - +
48D GLU* 3.7 7.6 + - - +
50D ILE* 1.3 78.7 - - - +
52D TRP* 1.3 64.1 + - - +
54D LYS* 3.3 13.1 + - - +
55D GLU* 3.2 43.9 + - - +
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Residues in contact with TRP 52 (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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2D SER* 3.5 30.6 - - - -
5D VAL* 3.5 31.4 - - + -
48D GLU 3.1 17.3 + - - +
49D ALA 3.6 2.0 - - - +
50D ILE 3.3 0.2 - - - -
51D ASN* 1.3 75.1 - - - +
53D LEU* 1.3 67.6 + - + +
55D GLU* 3.2 11.4 + - - +
56D GLN* 2.8 52.7 + - + +
138D LEU* 3.5 29.4 - - + -
141D GLU* 4.0 17.0 - - + -
142D ALA* 3.6 20.6 - - + -
145D LYS* 4.1 21.7 - - + +
146D PHE* 3.3 32.7 - + + -
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Residues in contact with LEU 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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45D PHE* 4.4 6.7 - - + -
49D ALA 3.0 22.0 + - - +
50D ILE* 3.5 9.2 - - - +
52D TRP* 1.3 79.5 - - + +
54D LYS* 1.3 60.0 + - - +
56D GLN* 3.1 1.5 + - + +
57D PHE* 2.8 57.5 + - + -
103D PHE* 3.7 19.1 - - + -
117D LEU* 3.9 27.8 - - + -
138D LEU* 3.7 29.6 - - + +
139D ILE* 3.9 10.5 - - + -
142D ALA* 3.7 17.5 - - + -
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Residues in contact with LYS 54 (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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50D ILE* 2.9 34.6 + - + +
51D ASN* 3.6 14.1 - - - +
53D LEU* 1.3 75.0 - - - +
55D GLU* 1.3 63.4 + - + +
57D PHE* 3.9 3.1 - - - +
58D SER* 3.1 22.9 + - - -
103D PHE* 3.5 47.2 + - + -
104D THR* 4.8 4.6 - - - +
105D SER* 5.8 0.8 + - - -
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Residues in contact with GLU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0D HIS 4.6 3.0 - - - +
1D MSE 3.8 32.8 - - + +
2D SER* 2.7 43.4 + - - +
51D ASN* 3.2 33.7 + - - +
52D TRP* 3.2 11.5 + - - +
54D LYS* 1.3 77.0 - - + +
56D GLN* 1.3 63.0 + - - +
58D SER* 2.6 26.5 + - - -
59D TYR* 3.0 23.8 + - - +
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Residues in contact with GLN 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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2D SER* 2.9 27.7 + - - -
3D GLU 3.0 20.8 + - - -
4D PRO* 3.6 3.3 - - - +
5D VAL* 2.9 28.4 + - - +
6D ILE 4.5 1.0 + - - -
52D TRP* 2.8 58.5 + - + +
53D LEU* 3.8 4.3 - - - +
55D GLU* 1.3 73.2 - - - +
57D PHE* 1.3 64.5 + - - +
59D TYR* 3.1 21.6 + - - +
60D LEU* 3.4 15.9 + - - +
138D LEU* 3.9 21.2 - - + +
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Residues in contact with PHE 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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53D LEU* 2.8 42.5 + - + +
54D LYS* 3.9 3.8 - - - +
56D GLN* 1.3 72.2 - - - +
58D SER* 1.3 61.9 + - - +
60D LEU* 3.2 26.1 + - - +
97D PRO* 3.5 12.5 - - + +
101D ILE* 4.1 25.6 - - + -
103D PHE* 3.6 37.5 - + + -
119D ILE* 3.9 19.5 - - + -
135D LEU* 3.4 30.5 - - + -
138D LEU* 3.9 17.0 - - + -
139D ILE* 4.0 21.8 - - + -
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Residues in contact with SER 58 (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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1D MSE 5.5 2.9 - - - +
54D LYS 3.1 10.5 + - - -
55D GLU* 2.6 23.6 + - - -
57D PHE* 1.3 81.1 - - - +
59D TYR* 1.3 68.9 + - - +
61D GLY* 3.2 14.9 + - - -
62D ASN* 4.4 5.6 + - - -
97D PRO* 3.9 11.0 - - - +
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Residues in contact with TYR 59 (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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1D MSE 3.1 38.4 - - + +
2D SER* 2.7 33.9 + - - -
4D PRO* 3.7 40.6 - - + -
6D ILE 5.7 2.0 - - - +
55D GLU* 3.0 23.6 + - + +
56D GLN* 3.1 28.2 + - - +
58D SER* 1.3 82.4 + - - +
60D LEU* 1.3 66.8 + - + +
61D GLY 3.0 2.9 - - - -
62D ASN* 3.0 35.7 + - - +
63D LEU* 3.9 8.2 + - - +
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Residues in contact with LEU 60 (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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6D ILE* 4.1 27.4 - - + +
56D GLN 3.7 9.0 - - - +
57D PHE* 3.3 17.9 - - - +
58D SER 3.2 0.6 - - - -
59D TYR* 1.3 77.6 - - + +
61D GLY* 1.3 59.5 + - - +
62D ASN 3.4 0.7 + - - -
63D LEU* 3.4 38.1 + - + +
95D LEU* 3.8 27.1 - - + +
97D PRO* 4.6 4.5 - - + -
101D ILE* 4.7 0.4 - - + -
131D TYR* 4.2 19.1 - - + -
134D PRO* 4.4 15.9 - - + -
135D LEU* 3.8 28.3 - - + -
138D LEU* 4.5 4.7 - - + -
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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