Contacts of the helix formed by residues 80 - 92 (chain B) in PDB entry 3UGV
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 ALA 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B PRO* 2.9 16.3 + - + +
79B LEU* 1.3 72.9 - - - +
81B PRO* 1.3 59.9 - - + -
82B ALA* 3.3 2.2 - - + +
83B GLU* 3.1 29.1 + - + +
84B ILE* 2.8 37.5 + - - +
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Residues in contact with PRO 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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79B LEU 3.9 5.2 - - - +
80B ALA* 1.3 82.2 - - - +
82B ALA* 1.3 52.6 + - - +
84B ILE* 3.6 2.7 - - + +
85B TYR* 2.7 37.9 + - - +
109B ASP* 4.1 4.4 - - - +
112B VAL* 3.3 33.1 - - + +
113B TRP* 3.3 55.6 - - + +
116B LEU* 4.2 17.0 - - + -
285B SER* 4.3 1.8 - - - +
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Residues in contact with ALA 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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80B ALA* 3.3 1.2 - - + -
81B PRO* 1.3 79.4 - - - +
83B GLU* 1.3 65.6 + - + +
85B TYR* 3.4 8.2 + - - +
86B ASP* 3.2 21.3 + - - +
113B TRP* 5.1 5.1 - - + -
285B SER* 4.7 5.4 + - - +
289B ARG* 4.6 17.4 + - - +
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Residues in contact with GLU 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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78B PRO* 4.7 15.7 - - - +
80B ALA* 3.1 25.7 + - + +
82B ALA* 1.3 79.6 - - + +
84B ILE* 1.3 62.2 + - + +
86B ASP* 3.2 8.7 + - - +
87B LYS* 3.1 49.0 + - - +
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Residues in contact with ILE 84 (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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7B PHE* 4.6 12.8 - - + -
74B LEU* 3.9 24.7 - - + -
77B GLN* 6.1 0.7 - - + -
78B PRO 4.1 13.5 - - - +
79B LEU* 4.1 6.3 - - + -
80B ALA 2.8 36.2 + - - +
81B PRO* 3.6 4.9 - - + +
83B GLU* 1.3 73.8 - - + +
85B TYR* 1.3 58.8 + - - +
87B LYS* 3.0 11.6 + - + +
88B THR* 2.8 34.3 + - + +
108B VAL* 3.8 26.7 - - + -
109B ASP* 5.7 2.9 - - - +
112B VAL* 3.6 26.7 - - + -
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Residues in contact with TYR 85 (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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81B PRO 2.7 21.9 + - - +
82B ALA* 3.6 6.1 - - - +
83B GLU 3.3 0.2 - - - -
84B ILE* 1.3 73.7 - - - +
86B ASP* 1.3 64.5 + - + +
88B THR* 3.2 15.8 + - - -
89B ARG* 3.3 58.2 + - + +
102B MET* 3.8 12.1 - - + +
105B ALA* 5.0 5.6 - - + -
109B ASP* 4.1 20.6 - - + +
259B PRO* 4.6 8.0 - - - +
281B ILE 4.2 4.9 + - - -
282B GLY* 3.5 33.6 - - - -
285B SER* 4.2 7.9 - - - +
286B GLY* 4.4 7.5 - - - -
289B ARG* 3.4 36.1 - - - -
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Residues in contact with ASP 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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82B ALA 3.2 9.1 + - - +
83B GLU* 3.5 11.0 - - - +
84B ILE 3.2 0.8 - - - -
85B TYR* 1.3 83.7 - - + +
87B LYS* 1.3 62.7 + - + +
89B ARG* 3.9 2.0 - - - +
90B LYS* 2.9 64.3 + - - +
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Residues in contact with LYS 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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73B MET* 4.0 16.9 - - + +
74B LEU* 4.3 9.6 - - + +
77B GLN* 3.3 43.9 + - - +
78B PRO* 4.7 6.1 + - - +
83B GLU* 3.1 38.8 + - - +
84B ILE* 3.0 8.1 + - - +
86B ASP* 1.3 83.6 - - - +
88B THR* 1.3 63.3 + - - +
90B LYS* 3.9 5.1 - - - +
91B SER* 3.0 26.0 + - - -
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Residues in contact with THR 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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70B MET* 3.7 34.1 - - + +
73B MET* 4.0 16.8 - - + -
74B LEU* 4.1 6.7 - - + -
84B ILE* 2.8 40.9 + - + +
85B TYR* 3.2 14.0 + - - -
87B LYS* 1.3 71.5 - - - +
89B ARG* 1.3 59.6 + - - +
91B SER* 2.8 20.4 + - - -
92B LEU* 3.8 5.7 + - - +
101B SER 5.5 0.3 - - - +
105B ALA* 3.3 25.3 + - + +
108B VAL* 4.4 6.1 - - + -
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Residues in contact with ARG 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 TYR* 3.3 54.8 + - - +
86B ASP* 4.1 2.7 - - - +
87B LYS 3.2 0.4 - - - -
88B THR* 1.3 75.0 + - - +
90B LYS* 1.3 65.2 + - + +
91B SER 3.2 1.1 - - - -
92B LEU* 3.2 5.8 + - - +
93B HIS 3.2 16.5 + - - -
96B GLY 5.5 0.2 - - - +
97B TYR* 3.8 55.4 + - + +
101B SER* 5.5 3.6 - - - +
102B MET* 3.5 33.6 - - + +
105B ALA* 4.0 17.3 - - + -
257B TYR 4.7 8.1 + - - -
258B GLY* 5.1 3.8 - - - -
259B PRO* 6.1 0.4 - - - +
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Residues in contact with LYS 90 (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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86B ASP* 2.9 54.1 + - - +
87B LYS* 3.9 5.4 - - - +
89B ARG* 1.3 75.3 - - + +
91B SER* 1.3 65.2 + - - +
92B LEU 3.1 0.9 + - - -
93B HIS* 2.9 31.1 + - + +
97B TYR* 4.0 23.2 + - + +
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Residues in contact with SER 91 (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 MET* 4.9 4.5 - - - +
73B MET* 3.6 22.6 - - - +
87B LYS 3.0 15.7 + - - -
88B THR* 2.8 23.2 + - - -
90B LYS* 1.3 77.9 - - - +
92B LEU* 1.3 73.0 + - - +
93B HIS* 3.9 0.5 + - - -
94B PHE* 5.3 4.2 + - - +
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Residues in contact with LEU 92 (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 ALA* 5.2 10.5 - - + -
70B MET* 3.8 25.4 - - + -
88B THR 3.8 5.3 + - - +
89B ARG* 3.2 6.3 + - - +
90B LYS 3.1 0.6 - - - -
91B SER* 1.3 94.0 + - - +
93B HIS* 1.3 65.2 + - - +
94B PHE* 3.1 3.4 - - - -
95B VAL* 2.9 30.6 + - + +
96B GLY 3.4 10.2 + - - +
101B SER* 3.9 32.8 - - - +
104B ALA* 5.1 2.5 - - + -
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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