Contacts of the helix formed by residues 59 - 78 (chain B) in PDB entry 2AGV
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 ASP 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLU 4.5 0.6 + - - -
56B GLN 5.2 1.1 - - - +
57B PHE 3.6 0.6 - - - -
58B GLU* 1.3 82.8 - - - +
60B LEU* 1.3 69.0 + - - +
61B LEU* 3.1 21.7 + - - +
62B VAL* 3.1 30.7 + - + +
63B ARG* 3.2 9.5 - - - +
254B ASP* 5.0 7.6 - - - +
1104B BHQ 2.6 33.9 + - - +
1111B PTY 5.2 5.8 - - - +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU 3.6 2.1 + - - -
59B ASP* 1.3 79.4 + - - +
61B LEU* 1.3 66.9 + - + +
63B ARG* 3.4 11.7 + - + +
64B ILE* 3.1 35.4 + - + +
257B GLY* 5.0 4.0 - - - -
258B GLU* 3.3 43.1 - - + +
261B SER* 3.3 29.6 - - - +
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ASP* 3.1 11.7 + - - +
60B LEU* 1.3 76.2 - - + +
62B VAL* 1.3 61.4 + - - +
63B ARG 3.1 2.2 - - - -
64B ILE* 3.6 11.3 - - + +
65B LEU* 3.0 32.4 + - - +
257B GLY* 4.0 30.5 - - - +
260B LEU* 3.8 18.2 - - + -
261B SER* 4.9 2.9 - - - +
264B ILE* 5.9 0.2 - - + -
307B ILE* 3.3 32.2 - - + +
308B PRO* 5.5 0.2 - - + -
1104B BHQ 3.7 55.4 - - + +
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLN 4.1 2.5 - - - +
57B PHE* 3.7 28.1 - - + +
59B ASP* 3.1 37.7 + - + +
61B LEU* 1.3 75.7 - - - +
63B ARG* 1.3 57.4 + - - +
66B LEU* 2.9 27.9 + - - +
98B LEU* 3.7 16.9 - - + +
101B ASN* 3.4 26.5 - - - +
1104B BHQ 3.3 33.7 - - + +
1111B PTY 5.7 0.4 - - - +
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE 5.8 0.4 + - - -
57B PHE* 3.3 26.2 + - + +
58B GLU* 3.6 24.7 + - - +
59B ASP 3.2 18.3 + - - +
60B LEU* 3.5 15.9 - - + +
61B LEU 3.1 0.4 - - - -
62B VAL* 1.3 76.9 - - - +
64B ILE* 1.3 61.6 + - + +
65B LEU 3.2 0.2 - - - -
66B LEU* 3.1 17.6 + - + +
67B LEU* 2.8 31.7 + - - +
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.1 26.9 + - + +
61B LEU* 3.6 16.4 - - + +
63B ARG* 1.3 76.7 - - + +
65B LEU* 1.3 59.8 + - + +
67B LEU* 3.4 10.5 + - + +
68B ALA* 2.9 25.8 + - - +
261B SER* 3.7 24.2 - - - +
264B ILE* 4.2 22.9 - - + -
303B ALA* 3.9 24.2 - - + +
307B ILE* 5.3 2.9 - - + -
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU 3.0 17.5 + - - +
62B VAL 4.0 3.6 - - - +
64B ILE* 1.3 75.8 - - - +
66B LEU* 1.3 56.3 + - - +
68B ALA* 3.0 4.5 + - + +
69B ALA* 2.7 35.9 + - - +
94B ILE* 4.0 16.3 - - + +
97B ILE* 5.2 7.0 - - + -
98B LEU* 4.0 17.0 - - + -
303B ALA* 4.2 24.0 - - + +
304B VAL* 4.5 19.1 - - + -
307B ILE* 4.3 14.6 - - + -
309B GLU* 4.7 9.4 - - + +
793B LEU* 6.2 0.7 - - + -
1104B BHQ 3.5 37.0 - - + -
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 4.0 26.7 - - + -
62B VAL 2.9 21.1 + - - +
63B ARG* 3.4 19.3 - - + +
65B LEU* 1.3 76.3 - - - +
67B LEU* 1.3 64.1 + - - +
69B ALA* 3.1 7.5 + - + +
70B CYS* 3.1 28.0 + - - -
95B LEU* 6.0 5.4 - - + -
98B LEU* 3.6 22.6 - - + +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ARG 2.8 20.2 + - - +
64B ILE* 3.6 9.6 - - + +
66B LEU* 1.3 73.5 - - - +
68B ALA* 1.3 56.7 + - - +
70B CYS* 2.6 36.1 + - + +
71B ILE* 3.0 33.4 + - + -
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE 2.9 14.5 + - - +
65B LEU* 3.4 13.7 - - + +
67B LEU* 1.3 77.4 - - - +
69B ALA* 1.3 56.4 + - - +
71B ILE* 3.4 8.6 + - - -
72B SER* 2.9 30.0 + - - -
94B ILE* 4.7 5.8 - - + +
299B ALA 5.7 0.2 - - - -
300B VAL* 3.7 22.1 - - + +
303B ALA* 3.9 23.1 - - + -
304B VAL* 5.3 0.7 - - + -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU 2.7 16.0 + - - +
66B LEU* 3.2 16.4 - - + +
68B ALA* 1.3 71.8 - - - +
70B CYS* 1.3 54.7 + - - +
72B SER* 3.3 7.9 + - - -
73B PHE* 2.7 35.6 + - - +
91B PRO* 4.2 7.4 - - - +
94B ILE* 3.7 25.3 - - + +
95B LEU* 4.6 15.0 - - + +
98B LEU* 4.9 1.8 - - + -
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Residues in contact with CYS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU* 3.1 25.6 + - - -
67B LEU* 2.6 26.4 + - + +
69B ALA* 1.3 69.6 - - - +
71B ILE* 1.3 59.0 + - + +
73B PHE* 3.2 7.2 + - - +
74B VAL* 2.8 38.0 + - + +
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Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.0 35.6 + - + +
68B ALA* 3.7 8.1 - - - +
70B CYS* 1.3 76.3 - - + +
72B SER* 1.3 53.4 + - - +
74B VAL* 3.2 7.0 + - + +
75B LEU* 2.8 50.9 + - + +
296B PHE* 3.6 55.2 - - + +
299B ALA* 5.8 4.3 - - + -
300B VAL* 4.1 7.9 - - + -
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Residues in contact with SER 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA 2.9 19.5 + - - -
69B ALA* 3.4 8.5 - - - -
71B ILE* 1.3 77.6 - - - +
73B PHE* 1.3 56.2 + - - +
75B LEU* 3.4 6.0 + - - +
76B ALA* 2.9 30.0 + - - +
90B GLU* 2.8 41.5 + - - +
91B PRO* 3.3 15.7 - - - +
94B ILE* 4.4 4.3 - - - -
300B VAL* 4.1 7.3 - - - +
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Residues in contact with PHE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ALA 2.7 19.7 + - - +
70B CYS* 3.5 9.6 - - - +
72B SER* 1.3 74.4 + - - +
74B VAL* 1.3 71.3 + - + +
76B ALA* 3.3 3.8 + - - +
77B TRP* 3.1 45.7 + + + +
88B PHE* 3.9 27.3 - + - -
91B PRO* 3.8 16.1 - - + +
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Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B CYS* 2.8 24.6 + - + +
71B ILE* 3.6 7.6 - - + +
73B PHE* 1.3 82.4 - - + +
75B LEU* 1.3 67.2 + - + +
77B TRP* 3.0 7.3 + - + +
78B PHE* 2.8 39.0 + - + +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ILE* 2.8 44.8 + - + +
72B SER* 3.7 7.2 - - - +
74B VAL* 1.3 79.2 - - + +
76B ALA* 1.3 63.7 + - - +
77B TRP 2.9 5.9 + - - -
78B PHE* 3.7 9.5 + - - +
79B GLU* 3.6 19.8 - - - +
90B GLU* 5.8 2.2 - - - +
293B ILE* 4.3 21.5 - - + +
296B PHE* 4.2 15.7 - - + +
297B LYS* 3.9 50.9 - - + +
300B VAL* 5.2 3.4 - - + -
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B SER 2.9 18.7 + - - +
73B PHE 3.6 1.1 - - - +
75B LEU* 1.3 76.2 - - - +
77B TRP* 1.3 60.2 + - - +
79B GLU* 4.1 17.7 - - - +
87B ALA* 3.2 36.4 - - - +
88B PHE* 3.4 29.3 - - + -
91B PRO* 4.3 3.8 - - + -
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Residues in contact with TRP 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B PHE* 3.1 31.1 + + + +
74B VAL* 3.0 12.1 + - + +
75B LEU 2.9 1.2 - - - -
76B ALA* 1.3 79.8 - - - +
78B PHE* 1.3 61.2 + + + +
79B GLU* 2.6 22.5 + - - +
88B PHE* 3.5 30.1 - + + -
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Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 2.8 25.8 + - + +
75B LEU* 3.7 8.9 - - - +
77B TRP* 1.3 77.9 - + + +
79B GLU* 1.3 58.8 + - - +
289B ILE* 3.5 37.7 - - + -
293B ILE* 4.6 17.3 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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