Contacts of the helix formed by residues 82 - 93 (chain B) in PDB entry 2PYO
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 THR 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A GLN* 3.4 27.4 - - + +
88A ALA* 3.6 2.9 - - - -
78B ARG* 3.1 30.0 + - - +
80B THR* 3.5 8.1 - - + +
81B VAL* 1.3 76.3 - - - +
83B ALA* 1.3 65.7 + - - +
84B MET* 3.5 9.8 + - - +
85B ASP* 2.9 39.4 + - - +
86B VAL* 3.0 13.2 + - - +
28J C 6.0 3.1 - - - -
29J A 5.9 3.1 - - - +
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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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85A GLN* 3.1 8.9 + - - +
87A SER* 3.6 28.7 - - - +
88A ALA* 3.6 17.9 - - - +
91A ALA* 4.9 1.0 - - + +
82B THR* 1.3 73.1 - - - +
84B MET* 1.3 52.2 + - + +
86B VAL* 2.9 7.2 + - - +
87B VAL* 2.7 38.7 + - - +
100B PHE* 3.8 25.1 - - + +
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Residues in contact with MET 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B THR* 3.2 8.4 + - - +
83B ALA* 1.3 74.8 - - + +
85B ASP* 1.3 61.8 + - - +
87B VAL* 4.1 8.3 - - + -
88B TYR* 2.7 87.4 + - + +
100B PHE 4.0 4.3 - - - +
101B GLY* 3.5 30.1 - - - +
102B GLY* 3.5 25.8 - - - +
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Residues in contact with ASP 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ALA* 3.8 19.1 - - - +
72B TYR* 3.9 13.9 - - + +
73B THR* 2.9 22.4 + - - +
78B ARG* 2.7 44.5 + - - -
81B VAL* 4.2 4.9 - - + -
82B THR* 2.9 29.2 + - - +
84B MET* 1.3 77.4 - - - +
86B VAL* 1.3 58.1 + - - +
88B TYR* 3.8 7.0 - - - +
89B ALA* 2.9 28.2 + - - +
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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
----------------------------------------------------------
88A ALA* 4.0 16.8 - - + -
91A ALA* 3.7 23.8 - - + -
92A LEU* 3.6 37.5 - - + +
65B VAL* 4.6 1.3 - - + -
69B ALA* 4.2 6.7 - - + -
81B VAL* 4.0 13.5 - - + -
82B THR 3.0 11.2 + - - +
83B ALA 2.9 8.4 + - - +
85B ASP* 1.3 74.9 - - - +
87B VAL* 1.3 55.5 + - - +
89B ALA* 2.8 9.3 + - - +
90B LEU* 2.7 46.0 + - + +
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA* 5.0 1.1 - - + -
83B ALA 2.7 23.2 + - - +
84B MET* 3.8 18.8 - - + +
86B VAL* 1.3 70.9 - - - +
88B TYR* 1.3 68.5 + - + +
90B LEU* 3.3 8.4 + - - +
91B LYS* 3.0 31.6 + - + +
97B LEU* 4.4 30.9 + - + +
100B PHE* 4.0 26.9 - - + -
101B GLY 4.2 18.6 - - - +
102B GLY* 4.6 5.4 - - - +
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Residues in contact with TYR 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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72B TYR* 3.7 25.6 + + + +
84B MET* 2.7 64.1 + - + +
85B ASP* 3.8 8.3 - - - +
87B VAL* 1.3 78.5 - - + +
89B ALA* 1.3 62.0 + - - +
91B LYS* 3.8 15.9 - - - +
92B ARG* 3.3 23.7 + - - +
102B GLY* 5.6 1.6 - - - -
80D TYR* 3.3 74.8 + + + +
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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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65B VAL* 3.4 32.3 - - + +
68B ASP* 3.9 6.1 - - + -
69B ALA* 3.6 14.4 - - + +
72B TYR* 3.8 8.3 - - - -
85B ASP 2.9 14.8 + - - +
86B VAL 2.8 10.0 + - - +
88B TYR* 1.3 78.3 - - - +
90B LEU* 1.3 61.3 + - - +
92B ARG* 3.4 10.8 - - - +
93B GLN* 3.1 22.8 - - - +
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Residues in contact with LEU 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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91A ALA 4.6 0.2 - - - +
92A LEU* 5.7 0.2 - - + -
95A ALA* 3.6 28.0 - - + -
61B PHE* 4.3 6.3 - - + -
65B VAL* 3.7 33.4 - - + -
86B VAL* 2.7 32.5 + - + +
87B VAL* 3.7 4.9 - - - +
89B ALA* 1.3 73.6 - - - +
91B LYS* 1.3 59.9 + - - +
93B GLN* 3.0 12.0 + - + +
95B ARG* 2.9 46.9 + - + +
97B LEU* 3.5 40.8 - - + +
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Residues in contact with LYS 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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87B VAL* 3.0 27.0 + - - +
88B TYR* 3.8 15.3 - - - +
90B LEU* 1.3 77.4 - - - +
92B ARG* 1.3 61.5 + - - +
94B GLY* 3.1 14.4 + - - -
96B THR* 4.2 37.6 + - - +
102B GLY* 5.2 8.7 + - - -
76D ARG* 6.1 2.9 - - - -
80D TYR* 4.6 16.4 + - - +
65H ASP* 5.4 7.4 + - - +
68H GLU* 3.2 26.5 + - - -
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Residues in contact with ARG 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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68B ASP* 3.1 28.5 + - - +
72B TYR* 3.4 25.2 + - - +
88B TYR 3.3 5.4 + - - +
89B ALA 3.4 11.2 - - - +
91B LYS* 1.3 77.9 - - - +
93B GLN* 1.3 59.8 + - - +
94B GLY 3.0 8.1 + - - -
73D GLU* 3.3 26.8 + - - +
76D ARG* 6.0 0.9 - - - +
97D LEU* 3.1 35.7 + - - +
98D LEU* 3.0 37.6 - - - +
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Residues in contact with GLN 93 (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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61B PHE* 6.4 0.2 - - + -
64B ASN* 3.4 31.0 - - - +
65B VAL* 4.5 15.9 - - + -
68B ASP* 3.0 23.0 - - - +
89B ALA 3.1 18.4 - - - +
90B LEU* 3.0 10.8 + - - +
92B ARG* 1.3 79.7 + - - +
94B GLY* 1.3 61.6 + - - +
95B ARG* 3.2 15.9 + - + +
94C LYS* 5.8 4.0 - - - +
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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