Contacts of the helix formed by residues 56 - 68 (chain A) in PDB entry 1VEG
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A LEU* 3.6 4.0 + - - +
53A PHE* 3.3 9.8 + - - +
55A GLY* 1.3 79.3 + - - +
57A VAL* 1.3 67.1 + - - +
58A GLN* 4.9 5.7 - - - +
59A LEU* 3.3 45.2 - - + +
60A ALA* 2.9 27.0 + - - +
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Residues in contact with VAL 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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32A SER* 3.2 51.1 - - - +
35A GLN* 4.9 10.8 - - + -
36A LEU* 3.7 15.4 - - + +
39A MET* 5.2 3.4 - - + -
50A LEU* 3.5 10.6 - - + +
55A GLY 3.8 1.4 + - - +
56A ASN* 1.3 71.7 - - - +
58A GLN* 1.3 59.5 + - + +
60A ALA* 3.5 4.2 - - - +
61A ALA* 3.0 26.7 + - + +
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Residues in contact with GLN 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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56A ASN* 3.1 6.2 - - - +
57A VAL* 1.3 77.6 - - + +
59A LEU* 1.3 68.5 + - + +
60A ALA 2.9 1.3 - - - -
61A ALA* 2.7 9.0 + - + -
62A GLN* 2.5 50.3 + - + +
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Residues in contact with LEU 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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53A PHE* 3.5 28.3 - - + +
56A ASN* 3.3 40.2 + - + +
58A GLN* 1.3 83.9 - - + +
60A ALA* 1.3 64.4 - - - +
62A GLN* 3.5 21.6 - - - +
63A THR* 3.3 21.1 + - - -
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Residues in contact with ALA 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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36A LEU* 4.0 14.6 - - + -
49A ALA* 3.8 19.5 - - + -
50A LEU 4.3 4.5 - - - +
53A PHE* 3.4 23.2 - - + -
56A ASN 2.9 18.9 + - - +
57A VAL 3.5 4.5 - - - +
58A GLN 2.8 0.4 + - - -
59A LEU* 1.3 73.1 - - - +
61A ALA* 1.3 56.2 + - - +
63A THR* 2.9 6.4 + - - -
64A LEU* 2.5 38.1 + - + +
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Residues in contact with ALA 61 (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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36A LEU* 4.4 0.8 - - - +
39A MET* 3.1 43.7 - - + -
57A VAL* 3.0 15.0 + - + +
58A GLN* 2.7 12.1 + - + +
60A ALA* 1.3 67.4 - - - +
62A GLN* 1.3 53.1 + - - +
63A THR 2.5 12.5 + - - -
64A LEU* 4.0 7.0 - - - -
65A ALA* 2.5 37.1 + - + +
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Residues in contact with GLN 62 (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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58A GLN* 2.5 34.1 + - + +
59A LEU* 3.5 23.7 - - - +
61A ALA* 1.3 71.3 - - - +
63A THR* 1.3 57.4 + - - +
65A ALA* 4.7 2.6 - - - +
66A HIS* 3.2 24.0 + - - +
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Residues in contact with THR 63 (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 PHE* 3.4 30.7 - - + -
59A LEU 3.4 7.2 + - - -
60A ALA 2.9 6.8 + - - -
61A ALA 2.5 4.8 + - - -
62A GLN* 1.3 77.1 + - - +
64A LEU* 1.3 59.9 + - - +
65A ALA 3.0 1.5 + - - -
66A HIS* 3.1 3.3 + - - -
67A HIS* 2.7 47.3 + - + +
71A LEU* 5.1 1.1 - - + -
72A PRO* 3.8 30.7 - - + -
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Residues in contact with LEU 64 (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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36A LEU* 4.2 13.5 - - + -
41A PHE* 3.1 54.2 - - + -
45A VAL* 3.4 26.2 - - + -
46A ALA* 4.6 0.2 - - - -
49A ALA* 3.7 26.7 - - + -
60A ALA 2.5 21.0 + - - +
61A ALA* 3.9 1.6 - - - +
63A THR* 1.3 72.6 - - - +
65A ALA* 1.3 53.2 + - - +
67A HIS* 5.0 1.6 - - - -
68A GLY* 2.5 33.4 + - - +
69A GLY* 2.9 17.4 + - - +
70A SER 4.2 3.1 - - - +
71A LEU* 4.1 18.6 - - + +
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Residues in contact with ALA 65 (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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39A MET* 5.2 4.3 - - - -
41A PHE* 3.6 12.3 - - + -
61A ALA* 2.5 26.2 + - + +
62A GLN* 4.7 2.0 - - - +
64A LEU* 1.3 71.8 - - - +
66A HIS* 1.3 70.3 + - - +
67A HIS 3.4 0.5 - - - -
68A GLY* 3.0 13.7 + - - -
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Residues in contact with HIS 66 (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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62A GLN 3.2 21.3 + - - +
63A THR* 3.1 5.5 + - - +
65A ALA* 1.3 80.5 - - - +
67A HIS* 1.3 72.9 - + + +
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Residues in contact with HIS 67 (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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63A THR* 2.7 26.6 + - + +
64A LEU 4.4 0.7 - - - +
65A ALA 3.4 0.2 - - - -
66A HIS* 1.3 84.2 - + - +
68A GLY* 1.3 62.3 + - - +
69A GLY 4.9 0.2 - - - +
70A SER* 4.6 9.8 + - - -
71A LEU 4.2 19.5 + - - +
72A PRO* 4.1 18.9 - - + +
73A PRO* 3.9 29.8 - - + +
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Residues in contact with GLY 68 (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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40A GLY 5.6 0.4 - - - -
41A PHE* 4.5 2.9 - - - -
64A LEU 2.5 20.3 + - - -
65A ALA* 3.0 9.1 + - - -
67A HIS* 1.3 75.8 - - - +
69A GLY* 1.3 70.0 + - - +
70A SER* 4.5 0.5 - - - -
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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