Contacts of the helix formed by residues 62 - 72 (chain A) in PDB entry 2VLA
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 LYS 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A VAL* 5.5 7.3 - - - +
49A ASN* 4.3 9.0 - - - +
60A THR 3.9 0.6 + - - -
61A THR* 1.3 73.8 - - - +
63A LYS* 1.3 57.2 + - - +
65A LEU* 3.2 11.9 + - + +
66A ASP* 2.8 59.4 + - - +
103L T 5.2 7.3 + - - -
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Residues in contact with LYS 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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61A THR* 3.2 11.0 + - - +
62A LYS* 1.3 79.4 - - - +
64A THR* 1.3 56.3 + - - +
66A ASP* 3.4 10.5 + - + +
67A ASN* 2.9 42.0 + - - +
104L A 3.5 22.6 - - - +
105L C 3.4 17.0 - - - +
206M G 4.0 10.8 - - + -
207M G 3.0 43.5 + - + +
208M G 2.7 32.1 + - - -
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Residues in contact with THR 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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56A LEU* 4.5 0.2 - - + -
60A THR* 3.5 18.8 - - + -
61A THR* 3.1 11.9 + - - -
63A LYS* 1.3 76.3 - - - +
65A LEU* 1.3 65.8 + - - +
67A ASN* 3.2 3.9 + - - +
68A HIS* 2.9 32.9 + - + +
205M C 3.2 49.7 - - + +
206M G 2.8 31.9 + - + -
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASN* 3.7 33.1 - - + +
52A LEU* 4.0 20.8 - - + +
53A ILE* 3.8 54.7 - - + +
56A LEU* 4.1 3.4 - - + -
60A THR* 3.9 15.9 - - + +
61A THR 3.1 19.5 + - - +
62A LYS* 3.6 13.7 - - + +
64A THR* 1.3 77.4 - - - +
66A ASP* 1.3 63.4 + - - +
68A HIS* 3.3 7.8 + - - +
69A ARG* 3.0 21.7 + - - +
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Residues in contact with ASP 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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45A VAL* 4.3 2.8 - - - +
49A ASN* 2.9 14.7 + - - -
62A LYS* 2.8 53.5 + - - +
63A LYS* 3.6 11.4 - - + +
65A LEU* 1.3 72.8 - - - +
67A ASN* 1.3 62.1 + - - +
69A ARG* 2.8 36.4 + - - +
70A THR* 2.9 34.4 + - + +
104L A 6.0 4.5 - - + +
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Residues in contact with ASN 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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17A LYS* 3.7 11.2 - - - +
63A LYS* 2.9 26.8 + - - +
64A THR* 3.7 5.6 - - - +
66A ASP* 1.3 75.9 - - - +
68A HIS* 1.3 60.5 + - - +
70A THR* 4.1 5.6 + - - -
71A GLU* 2.8 52.1 + - - +
104L A 4.6 4.2 - - - -
105L C 2.9 24.6 + - - +
106L C 3.7 3.2 - - - +
205M C 6.1 0.2 - - - +
206M G 3.1 22.6 + - - -
207M G 3.0 25.9 + - - -
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Residues in contact with HIS 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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17A LYS* 3.7 38.4 - - + +
25A LEU* 4.3 3.8 - - + -
29A TYR* 2.8 30.6 + - + +
48A PHE* 4.8 1.1 - - - -
52A LEU* 3.5 23.6 - - + +
56A LEU* 3.5 30.4 - - + +
64A THR* 2.9 31.4 + - + -
65A LEU 3.5 3.8 - - - +
67A ASN* 1.3 75.2 - - - +
69A ARG* 1.3 63.1 + - - +
72A ILE* 3.1 8.5 + - - +
73A ALA* 3.0 23.9 + - - +
205M C 2.9 28.3 + - - -
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Residues in contact with ARG 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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44A PHE* 3.7 31.7 - - + -
45A VAL* 3.6 35.5 - - - +
48A PHE* 3.5 46.2 - - + -
49A ASN* 2.9 17.0 + - - -
65A LEU 3.0 7.3 + - - +
66A ASP* 2.8 42.2 + - - +
68A HIS* 1.3 77.3 - - - +
70A THR* 1.3 79.3 + - - +
73A ALA* 3.6 0.3 - - - +
74A GLY 2.9 25.5 + - - -
80A PHE* 3.4 12.2 - - + -
104L A 3.9 12.1 + - - -
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Residues in contact with THR 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 ASP* 2.9 22.3 + - + +
67A ASN* 4.1 2.6 - - - -
69A ARG* 1.3 101.7 - - + +
71A GLU* 1.3 65.1 + - - +
74A GLY* 3.6 2.6 - - - -
75A LYS* 3.0 32.4 + - - +
80A PHE* 5.0 4.0 - - + -
104L A 3.4 31.9 - - + +
105L C 2.7 31.4 + - - -
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Residues in contact with GLU 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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14A ILE* 3.6 26.7 - - + +
15A ARG 4.7 1.6 + - - +
17A LYS* 2.9 33.3 + - - -
67A ASN* 2.8 29.2 + - - +
70A THR* 1.3 76.3 + - - +
72A ILE* 1.3 57.2 + - - +
75A LYS* 3.5 6.2 - - - +
76A LEU* 2.8 29.0 + - - +
105L C 3.5 41.2 - - + +
106L C 2.9 33.7 + - - -
107L C 4.2 3.6 + - - -
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Residues in contact with ILE 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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14A ILE* 3.9 10.3 - - + -
15A ARG 3.7 23.6 - - - +
16A GLY* 4.3 0.2 - - - -
17A LYS* 3.6 42.4 - - + +
18A ALA* 4.4 5.4 - - + +
29A TYR* 3.7 20.2 - - + +
68A HIS* 3.1 9.8 + - - +
71A GLU* 1.3 81.5 - - - +
73A ALA* 1.3 66.4 + - - +
74A GLY 3.3 1.0 + - - -
76A LEU* 3.6 15.2 + - + -
77A PHE* 2.8 62.7 + - + +
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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