Contacts of the helix formed by residues 66 - 78 (chain A) in PDB entry 2AVD
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 HIS 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ARG 3.4 4.8 + - - -
65A GLU* 1.3 71.2 - - - +
67A PRO* 1.4 82.2 - - + +
68A ALA* 2.9 41.6 + - + +
69A LEU* 2.9 17.8 + - + +
70A ARG 2.9 9.9 + - - -
122A LEU* 3.6 39.2 - - + +
149A GLN* 4.6 6.1 - - + -
150A ALA* 4.0 20.3 + - - +
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Residues in contact with PRO 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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65A GLU 3.5 4.4 - - - +
66A HIS* 1.4 97.5 - - + +
68A ALA* 1.3 56.1 + - - +
70A ARG* 3.4 11.9 + - + +
71A SER* 2.9 33.2 + - - +
149A GLN* 4.3 9.4 - - - +
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Residues in contact with ALA 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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66A HIS* 2.9 27.0 + - + +
67A PRO* 1.3 73.3 - - - +
69A LEU* 1.3 58.0 + - - +
71A SER 3.4 0.3 + - - -
72A LEU* 2.8 29.6 + - - +
118A LEU* 4.3 2.2 - - + -
146A LEU* 3.6 33.0 - - + +
149A GLN* 3.7 25.0 - - + +
150A ALA* 3.8 8.5 - - + -
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Residues in contact with LEU 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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65A GLU* 4.0 22.0 - - + -
66A HIS* 2.9 20.2 + - + +
68A ALA* 1.3 74.6 - - - +
70A ARG* 1.3 66.1 + - - +
72A LEU* 3.3 2.9 + - + +
73A ARG 3.0 18.2 + - - -
91A ALA* 5.7 0.7 - - + -
92A GLN* 6.4 1.1 - - - +
115A TYR* 3.3 61.6 - - + +
118A LEU* 3.8 18.7 - - + +
119A ALA* 3.7 31.4 - - + +
122A LEU* 4.3 10.8 - - + -
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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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65A GLU* 3.7 24.5 - - + +
66A HIS 2.9 10.6 + - - +
67A PRO* 3.5 13.2 + - + +
69A LEU* 1.3 77.5 - - - +
71A SER* 1.3 64.2 + - - +
73A ARG* 3.1 25.4 + - - +
74A LEU* 3.0 55.5 + - + +
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Residues in contact with SER 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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67A PRO* 2.9 17.5 + - - +
68A ALA* 4.3 1.1 - - - -
70A ARG* 1.3 83.0 + - - +
72A LEU* 1.3 58.0 + - - +
74A LEU* 3.4 8.5 + - - +
75A LEU* 2.9 31.5 + - - +
146A LEU* 3.5 24.5 - - - -
149A GLN* 4.8 5.4 + - - -
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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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68A ALA 2.8 20.1 + - - +
69A LEU* 3.3 7.8 + - - +
71A SER* 1.3 72.9 - - - +
73A ARG* 1.3 57.6 + - - +
75A LEU* 3.8 4.2 - - + +
76A THR* 2.8 45.7 + - - +
113A THR* 3.6 11.2 - - - +
114A GLY 3.6 33.9 - - - +
115A TYR* 3.6 13.5 - - + +
118A LEU* 4.1 12.3 - - + -
142A LEU* 4.7 1.6 - - + +
143A GLY* 3.5 25.4 - - - +
146A LEU* 3.7 18.5 - - + +
147A TRP* 4.1 11.2 - - + +
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Residues in contact with ARG 73 (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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65A GLU* 2.9 39.4 + - - -
69A LEU 3.0 7.0 + - - +
70A ARG* 3.1 25.6 + - - +
72A LEU* 1.3 74.7 - - - +
74A LEU* 1.3 84.5 + - - +
76A THR* 3.2 3.1 + - - -
77A LEU* 2.9 41.5 + - + +
85A MET* 3.7 26.7 - - + -
86A MET 6.0 0.2 - - - -
88A CYS* 4.0 26.4 - - - +
115A TYR* 3.6 18.5 - - + -
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Residues in contact with LEU 74 (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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70A ARG* 3.0 60.5 + - + +
71A SER* 3.9 6.1 - - - +
73A ARG* 1.3 100.3 - - + +
75A LEU* 1.3 63.1 + - - +
77A LEU* 3.2 19.4 + - + +
78A GLU* 3.3 18.9 + - - +
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Residues in contact with LEU 75 (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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71A SER 2.9 18.8 + - - +
72A LEU* 3.8 6.1 - - + +
74A LEU* 1.3 76.7 - - - +
76A THR* 1.3 62.5 + - - +
78A GLU* 3.1 13.5 + - + +
79A GLN* 3.0 38.5 + - - +
142A LEU* 3.7 31.4 - - + +
145A PRO* 6.4 0.2 - - + -
146A LEU* 3.7 24.2 - - + -
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Residues in contact with THR 76 (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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72A LEU* 2.8 25.4 + - - +
73A ARG 3.6 4.0 - - - -
75A LEU* 1.3 76.6 - - - +
77A LEU* 1.3 57.0 + - - +
79A GLN* 3.0 28.3 + - + +
82A GLY* 3.2 34.9 - - - +
85A MET* 3.8 15.1 - - - -
112A PHE* 3.6 18.4 - - + -
113A THR* 2.7 39.8 + - + +
142A LEU* 4.9 0.6 - - - +
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Residues in contact with LEU 77 (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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73A ARG* 2.9 48.2 + - + +
74A LEU* 3.2 11.9 + - + +
75A LEU 3.2 0.4 - - - -
76A THR* 1.3 75.5 - - - +
78A GLU* 1.3 64.1 + - - +
79A GLN 3.2 6.6 + - - +
82A GLY* 3.7 27.1 - - - +
83A ASP* 3.9 14.1 - - + +
85A MET* 3.7 10.5 - - + -
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Residues in contact with GLU 78 (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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74A LEU 3.3 14.0 + - - +
75A LEU* 3.1 16.5 + - + +
77A LEU* 1.3 82.4 - - - +
79A GLN* 1.3 69.0 + - - +
80A PRO* 4.3 2.9 - - - +
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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