Contacts of the helix formed by residues 46 - 60 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A PHE* 1.3 76.6 - - - +
47A LYS* 1.3 64.2 + - - +
48A GLU* 3.5 11.4 + - - +
49A ALA* 2.9 35.5 + - - +
50A ILE* 3.1 29.5 + - - +
113A THR 4.3 9.6 - - - +
114A HIS* 5.9 2.0 - - + +
115A TYR* 4.3 4.7 - - - -
146A PHE* 3.1 27.5 + - - +
147A VAL* 3.9 11.8 - - + +
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Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASN* 1.3 75.7 - - - +
48A GLU* 1.3 64.6 + - - +
50A ILE* 3.3 8.6 + - + +
51A ASN* 2.9 38.8 + - - +
113A THR 5.1 0.2 + - - -
115A TYR* 3.8 31.9 - - + +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASN* 3.2 12.3 + - - +
47A LYS* 1.3 81.2 - - - +
49A ALA* 1.3 63.0 + - - +
51A ASN* 3.3 6.6 + - - +
52A TRP* 3.1 22.9 + - - +
146A PHE* 3.3 43.1 - - + +
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 3.9 25.1 - - + -
46A ASN* 2.9 23.4 + - - +
48A GLU* 1.3 76.7 - - - +
50A ILE* 1.3 56.9 + - - +
52A TRP* 3.3 2.3 + - - +
53A LEU* 2.9 35.8 + - - +
142A ALA* 4.3 7.5 - - + +
146A PHE* 3.8 25.9 - - + +
147A VAL* 4.2 4.7 - - + -
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Residues in contact with ILE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 4.3 4.3 - - + -
46A ASN 3.1 18.4 + - - +
47A LYS* 3.3 7.4 + - + +
49A ALA* 1.3 75.4 - - - +
51A ASN* 1.3 64.5 + - - +
53A LEU* 3.2 7.8 + - - +
54A LYS* 2.9 30.7 + - + +
103A PHE* 3.9 16.1 - - + -
104A THR 6.2 0.2 - - - -
105A SER* 3.6 28.0 - - - +
115A TYR* 3.5 37.5 - - + -
117A LEU* 3.8 21.5 - - + -
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Residues in contact with ASN 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LYS* 2.9 32.7 + - - +
48A GLU* 3.8 6.0 - - - +
50A ILE* 1.3 83.9 - - - +
52A TRP* 1.3 61.6 + - - +
54A LYS* 3.4 12.8 + - - +
55A GLU* 3.2 21.0 + - - +
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Residues in contact with TRP 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 3.8 22.7 - - - -
3A GLU 5.2 0.8 + - - -
5A VAL* 3.6 31.6 - - + -
48A GLU 3.1 12.7 + - - +
49A ALA 3.7 1.8 - - - +
51A ASN* 1.3 73.3 - - - +
53A LEU* 1.3 67.9 + - + +
55A GLU* 3.2 8.4 + - - +
56A GLN* 2.9 59.6 + - + +
138A LEU* 3.6 30.1 - - + -
141A GLU* 4.1 15.0 - - + -
142A ALA* 3.7 22.0 - - + -
145A LYS* 4.1 18.8 - - + +
146A PHE* 3.4 37.4 - + + -
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 4.4 7.6 - - + -
49A ALA 2.9 24.7 + - - +
50A ILE* 3.5 5.6 - - - +
52A TRP* 1.3 82.4 - - + +
54A LYS* 1.3 63.3 + - - +
56A GLN* 4.4 1.3 - - + -
57A PHE* 2.8 51.3 + - + -
103A PHE* 3.9 16.4 - - + -
117A LEU* 4.0 26.7 - - + -
138A LEU* 3.6 36.3 - - + +
139A ILE* 3.9 8.3 - - + -
142A ALA* 3.7 17.7 - - + -
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Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 2.9 16.4 + - + +
51A ASN* 3.6 15.7 - - - +
52A TRP 3.3 0.2 - - - -
53A LEU* 1.3 74.0 - - - +
55A GLU* 1.3 63.3 + - - +
57A PHE* 3.6 3.5 + - - +
58A SER* 3.2 22.0 + - - -
103A PHE* 3.9 19.0 - - + -
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1A HIS* 2.8 35.4 + - - -
1A MSE 3.7 12.5 - - + +
2A SER* 2.6 34.4 + - - +
51A ASN 3.2 9.2 + - - +
52A TRP* 3.2 11.7 + - - +
53A LEU 3.2 0.4 - - - -
54A LYS* 1.3 81.0 - - - +
56A GLN* 1.3 61.3 + - - +
58A SER* 2.6 26.5 + - - +
59A TYR* 3.1 41.4 + - + +
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Residues in contact with GLN 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 2.8 25.8 + - - +
3A GLU 2.9 19.4 + - - -
4A PRO* 3.6 2.6 - - - +
5A VAL* 2.9 27.9 + - - +
6A ILE* 4.5 1.0 + - - +
52A TRP* 2.9 59.0 + - + +
53A LEU* 3.9 5.8 - - - +
55A GLU* 1.3 68.3 - - - +
57A PHE* 1.3 68.1 + - - +
59A TYR* 3.2 25.5 + - - +
60A LEU* 3.5 10.4 + - - +
138A LEU* 3.7 23.4 - - + +
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Residues in contact with PHE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 2.8 45.6 + - + +
54A LYS* 3.8 4.3 - - - +
56A GLN* 1.3 75.2 - - - +
58A SER* 1.3 64.5 + - - +
60A LEU* 3.1 24.7 + - - +
97A PRO* 3.6 11.7 - - + +
101A ILE* 4.1 21.1 - - + -
103A PHE* 3.5 46.2 - + + -
119A ILE* 4.1 22.0 - - + -
135A LEU* 3.5 29.6 - - + -
138A LEU* 3.9 17.0 - - + -
139A ILE* 4.1 9.2 - - + -
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Residues in contact with SER 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LYS 3.2 10.0 + - - -
55A GLU* 2.6 24.4 + - - +
57A PHE* 1.3 80.3 - - - +
59A TYR* 1.3 63.9 + - - +
61A GLY* 3.0 21.8 + - - -
62A ASN* 4.2 4.6 + - - +
97A PRO* 3.9 9.5 - - - +
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Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 3.5 30.5 - - + +
2A SER* 2.7 42.7 + - - -
4A PRO* 3.6 39.3 - - + -
6A ILE 5.7 2.2 - - - +
55A GLU* 3.1 41.1 + - + -
56A GLN* 3.4 20.6 - - - +
57A PHE 3.2 0.2 - - - -
58A SER* 1.3 84.8 + - - +
60A LEU* 1.3 67.5 + - + +
61A GLY 3.0 0.2 - - - -
62A ASN* 2.9 39.0 + - + +
63A LEU* 3.8 8.1 + - - +
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 4.0 39.7 - - + +
56A GLN 3.8 9.4 - - - +
57A PHE* 3.3 18.4 - - - +
58A SER 3.1 0.4 - - - -
59A TYR* 1.3 79.3 - - + +
61A GLY* 1.3 62.2 + - - +
62A ASN 3.2 0.9 + - - -
63A LEU* 3.4 27.4 + - + +
95A LEU* 3.8 27.2 - - + +
97A PRO* 4.5 4.3 - - + -
101A ILE* 4.7 0.7 - - + -
131A TYR* 4.1 18.8 - - + -
134A PRO* 4.3 14.6 - - + -
135A LEU* 3.8 29.8 - - + -
138A LEU* 4.4 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