Contacts of the helix formed by residues 64 - 72 (chain A) in PDB entry 2VGZ
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 GLY 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A THR* 4.2 7.9 - - - -
62A GLN* 3.7 6.4 + - - +
63A PHE* 1.3 77.7 - - - +
65A GLU* 1.3 66.0 + - - -
66A GLU 3.3 3.3 + - - -
67A MET* 3.3 7.7 + - - +
68A MET* 2.9 17.3 + - - +
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Residues in contact with GLU 65 (chain A).
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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49A LYS 3.7 13.0 - - - +
50A THR* 4.0 8.7 - - + +
64A GLY* 1.3 72.4 - - - +
66A GLU* 1.3 80.7 + - + +
68A MET* 3.6 3.1 + - - +
69A LYS* 3.3 34.5 + - - +
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Residues in contact with GLU 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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64A GLY 3.3 0.6 - - - -
65A GLU* 1.3 88.4 - - + +
67A MET* 1.3 65.0 + - - +
68A MET 3.2 2.0 - - - -
69A LYS* 3.3 40.2 + - - +
70A ARG* 3.2 19.9 + - - +
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Residues in contact with MET 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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62A GLN 5.0 2.2 - - - +
63A PHE* 3.7 29.8 - - + -
64A GLY 3.3 9.8 + - - +
66A GLU* 1.3 78.5 - - - +
68A MET* 1.3 58.2 + - - +
70A ARG* 3.4 19.4 + - - +
71A ALA* 2.9 25.6 + - - +
301A LEU* 4.1 27.4 - - + -
305A GLN* 3.5 25.6 - - + +
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Residues in contact with MET 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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48A PHE* 3.5 37.9 - - + +
49A LYS* 3.3 32.5 - - - +
50A THR* 3.8 21.1 - - - +
51A ALA* 3.9 5.4 - - + -
63A PHE* 4.1 14.7 - - + +
64A GLY 2.9 12.8 + - - +
65A GLU 3.7 2.9 - - - +
66A GLU 3.2 0.2 - - - -
67A MET* 1.3 74.5 - - - +
69A LYS* 1.3 65.2 + - - +
71A ALA* 3.1 2.9 + - - +
72A LEU* 3.0 35.3 + - + +
298A PHE* 3.6 36.1 - - + -
53B ILE* 4.1 6.3 - - + -
302B MET* 4.8 0.7 - - + -
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Residues in contact with LYS 69 (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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43A PRO* 4.0 38.0 - - + +
44A ASN* 3.3 32.7 + - - +
49A LYS* 6.4 0.9 - - - +
65A GLU* 3.3 22.7 + - - +
66A GLU* 3.3 42.6 + - - +
67A MET 3.4 0.2 - - - -
68A MET* 1.3 78.0 - - + +
70A ARG* 1.3 61.4 + - - +
72A LEU* 3.5 5.4 + - - -
73A GLN* 3.3 23.2 + - - +
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Residues in contact with ARG 70 (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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66A GLU 3.2 10.5 + - - +
67A MET* 3.6 20.8 - - - +
69A LYS* 1.3 79.0 - - - +
71A ALA* 1.3 62.1 + - - +
73A GLN* 3.2 18.6 + - - +
74A TYR 5.1 0.5 - - - +
80A ILE* 3.9 19.0 - - - +
81A PRO* 4.0 8.7 - - - +
82A GLU* 2.8 41.6 + - - -
297A THR* 3.4 14.8 - - + +
301A LEU* 3.7 30.5 - - + +
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Residues in contact with ALA 71 (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 PHE* 3.8 14.4 - - + -
67A MET 2.9 19.2 + - - +
68A MET* 3.1 6.7 + - - +
70A ARG* 1.3 73.4 - - - +
72A LEU* 1.3 58.7 + - - +
73A GLN 3.4 0.2 - - - -
297A THR* 3.5 5.8 - - - -
298A PHE* 3.1 51.2 + - + +
301A LEU* 3.7 19.9 - - + +
268B GLY 4.1 4.3 - - - -
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Residues in contact with LEU 72 (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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43A PRO 5.2 1.8 - - - +
46A PHE* 3.4 37.0 - - + -
48A PHE* 3.4 46.4 - - + +
68A MET* 3.0 26.1 + - + +
69A LYS* 4.1 5.6 - - - +
70A ARG 3.2 0.2 - - - -
71A ALA* 1.3 76.8 - - - +
73A GLN* 1.3 55.0 + - - +
298A PHE* 4.3 11.0 - - + -
266B SER* 2.6 30.2 + - - +
267B SER* 3.1 8.3 + - - -
268B GLY 2.7 16.4 + - - -
269B LEU* 4.0 22.0 - - + -
302B MET* 5.2 0.4 - - + -
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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