Contacts of the helix formed by residues 76 - 89 (chain B) in PDB entry 2YVE
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 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B ASP* 3.1 25.4 + - + +
75B GLU* 1.3 78.8 - - - +
77B PRO* 1.3 69.1 - - - +
78B LEU* 2.9 22.3 + - - +
79B GLU* 2.9 31.7 + - + +
80B ARG* 3.0 15.5 + - - +
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Residues in contact with PRO 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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75B GLU 3.3 11.4 - - - +
76B ASP* 1.3 86.1 - - - +
78B LEU* 1.3 64.0 + - + +
80B ARG* 3.7 13.9 - - + +
81B LEU* 2.9 27.5 + - - +
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Residues in contact with LEU 78 (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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76B ASP* 2.9 13.9 + - - +
77B PRO* 1.3 84.2 - - + +
79B GLU* 1.3 61.9 + - + +
81B LEU* 3.4 15.0 + - + +
82B ARG* 3.0 26.2 + - - +
132B HIS* 5.4 6.5 - - + +
136B VAL* 4.4 18.2 - - + -
173B ILE* 4.3 23.3 - - + +
174B PRO* 3.2 32.3 - - + +
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Residues in contact with GLU 79 (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 THR* 4.0 7.0 - - + +
72B ARG* 3.0 42.0 + - + +
73B ASP* 3.6 31.2 - - + +
76B ASP* 2.9 28.5 + - + +
78B LEU* 1.3 76.7 - - + +
80B ARG* 1.3 66.4 + - - +
82B ARG* 3.4 17.9 + - - +
83B ALA* 3.1 22.0 + - - +
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Residues in contact with ARG 80 (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 THR* 4.2 7.0 - - + -
74B PRO* 2.9 42.1 + - - +
75B GLU 5.1 0.2 - - - -
76B ASP 3.0 17.9 + - - +
77B PRO* 3.7 16.8 - - + +
79B GLU* 1.3 77.9 - - - +
81B LEU* 1.3 60.7 - - - +
83B ALA* 3.2 4.9 + - - +
84B VAL* 3.0 27.4 + - - +
119B GLN* 2.9 38.2 + - - +
120B TRP* 3.4 60.0 - - + +
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Residues in contact with LEU 81 (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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77B PRO 2.9 17.2 + - - +
78B LEU* 3.6 13.5 - - + +
79B GLU 3.2 0.2 - - - -
80B ARG* 1.3 74.5 - - - +
82B ARG* 1.3 66.0 + - - +
84B VAL* 3.1 9.1 + - + +
85B VAL* 2.9 29.6 + - + +
120B TRP 5.5 1.6 - - - -
122B PRO* 4.4 28.7 - - + -
136B VAL* 3.9 25.6 - - + +
139B VAL* 4.0 28.0 - - + -
140B GLN* 4.5 9.4 - - - +
173B ILE* 4.0 30.1 - - + -
174B PRO* 4.9 0.7 - - + -
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Residues in contact with ARG 82 (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 ARG* 3.3 34.2 - - - +
78B LEU 3.0 15.1 + - - +
79B GLU* 3.6 29.8 - - - +
81B LEU* 1.3 76.2 - - - +
83B ALA* 1.3 58.3 + - - +
85B VAL* 3.2 3.5 + - - +
86B VAL* 2.9 37.8 + - + +
170B LEU* 3.9 39.3 + - + +
173B ILE* 4.0 17.3 - - + +
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Residues in contact with ALA 83 (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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67B LEU* 3.8 11.0 - - + -
70B ILE* 3.7 25.5 - - + +
71B THR* 3.1 31.2 - - - +
79B GLU 3.1 10.2 + - - +
80B ARG 3.2 7.6 + - - +
82B ARG* 1.3 76.4 - - - +
84B VAL* 1.3 64.2 + - - +
86B VAL* 3.3 1.0 + - - -
87B THR* 2.9 28.6 + - - +
120B TRP* 4.7 0.2 - - + -
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TRP* 4.5 4.7 - - + -
67B LEU* 3.7 20.4 - - + -
80B ARG 3.0 18.1 + - - +
81B LEU* 3.5 11.0 - - + +
83B ALA* 1.3 75.9 - - - +
85B VAL* 1.3 65.9 + - + +
87B THR* 2.9 16.0 + - - -
88B LEU* 3.0 28.3 + - + +
120B TRP* 3.6 35.4 - - + +
121B ILE* 4.2 7.0 - - + -
140B GLN* 3.5 26.5 - - - +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 2.9 24.1 + - + +
82B ARG* 3.6 7.0 - - - +
84B VAL* 1.3 77.1 - - + +
86B VAL* 1.3 63.5 + - - +
88B LEU* 3.2 4.0 + - - +
89B ALA* 3.2 20.4 + - - +
139B VAL* 3.5 31.0 - - + -
140B GLN* 5.7 0.2 - - - -
143B ALA* 4.1 20.8 - - + +
146B LEU* 5.9 0.6 - - + +
166B LEU* 3.6 20.4 - - + -
169B ILE* 3.8 21.1 - - + -
170B LEU* 3.8 16.8 - - + -
173B ILE* 4.7 0.2 - - + -
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Residues in contact with VAL 86 (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 ILE* 3.9 19.5 - - + -
82B ARG* 2.9 36.3 + - + +
83B ALA* 3.8 4.0 - - - +
85B VAL* 1.3 76.3 - - - +
87B THR* 1.3 64.1 + - - +
89B ALA* 3.2 16.2 + - - +
90B GLU* 4.5 3.5 + - - +
166B LEU* 4.3 23.1 - - + +
170B LEU* 4.6 10.1 - - + -
1002B MBT 5.3 2.2 - - - -
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Residues in contact with THR 87 (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 TRP* 3.0 25.6 + - - +
66B GLU* 3.7 28.7 - - + -
67B LEU* 3.8 15.7 - - + +
70B ILE* 3.8 12.1 - - + -
83B ALA 2.9 18.9 + - - +
84B VAL* 2.9 20.3 + - - -
86B VAL* 1.3 76.9 - - - +
88B LEU* 1.3 60.0 + - - +
89B ALA 3.2 1.1 + - - -
90B GLU* 4.0 8.8 + - - +
1002B MBT 3.4 39.3 - - - -
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Residues in contact with LEU 88 (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 TRP* 4.8 2.0 - - + -
84B VAL* 3.0 28.8 + - + +
85B VAL 3.7 4.5 - - - +
86B VAL 3.2 0.2 - - - -
87B THR* 1.3 77.8 - - - +
89B ALA* 1.3 63.1 + - - +
90B GLU 3.2 5.1 + - - +
140B GLN* 3.6 15.9 - - - +
143B ALA* 3.7 25.0 - - + +
144B ASP* 3.4 21.3 - - - +
147B PHE* 3.2 51.6 + - + +
1002B MBT 3.4 41.1 - - + -
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Residues in contact with ALA 89 (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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85B VAL 3.2 9.6 + - - +
86B VAL 3.2 15.0 + - - +
88B LEU* 1.3 79.1 - - - +
90B GLU* 1.3 56.2 + - + +
146B LEU* 3.9 16.5 - - + +
162B ARG* 2.7 42.2 + - + +
166B LEU* 3.8 32.1 - - + -
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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