Contacts of the helix formed by residues 82 - 101 (chain B) in PDB entry 5D0Y
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 PHE 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B GLY 4.6 0.4 - - - +
81B PHE* 1.3 77.6 - - - +
83B ILE* 1.3 68.7 + - + +
84B GLY* 2.8 41.5 + - - -
85B PHE* 3.1 39.6 + + + -
129B TRP* 3.6 32.1 - + + -
132B MET* 4.4 21.5 - - + -
133B LEU* 3.7 31.6 - - + -
201B FOL 3.1 23.3 + - - +
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Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 5.8 2.7 - - + -
81B PHE* 3.8 30.5 - - + -
82B PHE* 1.3 80.8 - - + +
84B GLY* 1.3 63.7 + - - +
85B PHE 3.5 0.2 - - - -
86B THR* 3.3 25.9 - - + +
87B LEU* 3.5 6.9 + - - +
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Residues in contact with GLY 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PHE* 2.8 24.5 + - - -
83B ILE* 1.3 79.6 - - - +
85B PHE* 1.3 56.4 + - - +
86B THR 3.0 4.9 - - - -
87B LEU* 2.9 22.9 + - - +
88B THR 3.1 5.4 + - - -
129B TRP* 2.9 29.4 + - - -
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Residues in contact with PHE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASP* 4.0 4.4 - - - +
82B PHE* 3.1 13.6 + + + -
84B GLY* 1.3 74.0 - - - +
86B THR* 1.3 56.8 + - - +
88B THR* 3.5 5.5 - - - -
89B ALA* 3.1 27.0 + - - +
126B ASN* 3.7 33.2 - - + -
129B TRP* 3.7 26.2 - + + +
130B VAL* 4.2 8.3 - - + -
133B LEU* 3.5 28.3 - - + -
201B FOL 3.2 91.7 - + + +
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Residues in contact with THR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA* 3.7 31.5 - - + +
68B ASP* 2.6 25.0 + - - +
69B LEU* 4.7 12.1 - - + -
81B PHE* 3.7 14.6 - - - -
82B PHE 3.9 0.6 + - - -
83B ILE* 3.3 21.1 + - + -
84B GLY 3.0 0.4 - - - -
85B PHE* 1.3 77.1 - - - +
87B LEU* 1.3 63.2 + - - +
89B ALA* 3.2 4.0 + - - +
90B ALA* 3.2 20.3 + - - +
201B FOL 3.4 8.0 + - - -
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PHE* 4.0 26.2 - - + -
83B ILE 3.5 7.2 + - - +
84B GLY* 2.9 11.7 + - - +
86B THR* 1.3 78.6 - - - +
88B THR* 1.3 53.2 + - - +
90B ALA* 3.0 7.6 + - - +
91B LEU* 2.8 51.7 + - + +
125B LEU* 4.6 4.3 - - + -
129B TRP* 4.4 18.4 - - + -
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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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84B GLY 3.1 0.4 + - - -
85B PHE* 3.5 10.3 - - - +
87B LEU* 1.3 78.5 - - - +
89B ALA* 1.3 58.5 + - - +
90B ALA 3.0 0.2 + - - -
91B LEU* 3.1 5.6 + - - +
92B GLU* 2.8 38.1 + - + +
121B CYS* 3.9 23.7 - - + +
122B TYR* 5.2 3.6 - - + -
125B LEU* 3.8 13.6 - - - +
126B ASN* 3.0 29.1 + - - +
129B TRP* 2.9 26.9 + - - -
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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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26B LYS* 4.4 14.0 + - - +
64B GLY* 3.4 31.5 - - - +
68B ASP* 4.0 14.6 - - + +
85B PHE 3.1 14.2 + - - +
86B THR 3.2 4.0 + - - +
88B THR* 1.3 78.1 - - - +
90B ALA* 1.3 59.9 + - - +
92B GLU* 3.7 18.0 - - - +
93B SER* 3.5 13.9 + - - -
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Residues in contact with ALA 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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61B PHE* 3.4 56.7 - - + +
64B GLY 4.2 0.2 - - - -
65B ALA* 3.8 9.4 - - + +
86B THR 3.2 11.1 + - - +
87B LEU* 3.2 10.5 - - - +
89B ALA* 1.3 77.6 - - - +
91B LEU* 1.3 65.9 + - - +
93B SER* 3.5 1.0 + - - -
94B MET* 3.0 23.0 + - - +
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Residues in contact with LEU 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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61B PHE* 3.7 20.2 - - + -
87B LEU* 2.8 37.5 + - + +
88B THR 3.9 0.4 - - - +
90B ALA* 1.3 69.5 - - - +
92B GLU* 1.3 58.4 + - - +
94B MET* 2.9 21.8 + - + -
95B ILE* 2.8 42.3 + - + +
120B ILE* 5.2 7.4 - - + -
121B CYS* 3.9 14.6 - - - -
125B LEU* 3.6 30.5 - - + -
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Residues in contact with GLU 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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26B LYS* 3.7 17.8 + - - -
44B GLY 5.1 0.3 - - - -
45B PHE* 4.0 10.0 + - - +
48B SER* 3.4 22.5 + - - +
88B THR* 2.8 23.0 + - - +
89B ALA* 3.7 12.9 - - - +
91B LEU* 1.3 73.4 - - - +
93B SER* 1.3 60.4 + - - +
95B ILE* 3.5 6.2 + - - +
96B TYR* 3.0 30.5 + - + -
117B VAL* 4.2 8.7 - - + +
121B CYS* 3.5 15.3 - - + -
122B TYR* 2.6 38.0 + - + +
201B FOL 5.6 0.9 - - - +
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B SER* 2.5 40.5 + - - -
51B LEU* 3.3 13.7 - - - +
52B GLY* 3.4 25.6 - - - -
56B GLY 4.5 0.2 - - - +
60B GLY* 3.1 28.2 - - - -
64B GLY* 4.3 2.7 - - - -
89B ALA 3.5 12.5 + - - -
90B ALA 3.5 1.6 + - - -
91B LEU 3.2 0.6 - - - -
92B GLU* 1.3 80.1 - - - +
94B MET* 1.3 58.8 + - - +
95B ILE 3.5 0.2 - - - -
96B TYR* 4.1 0.8 + - - -
97B GLY* 3.5 2.8 + - - -
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Residues in contact with MET 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PRO* 3.3 40.8 - - + +
58B TRP* 4.9 10.3 - - + -
60B GLY 4.5 0.4 + - - -
61B PHE* 3.8 19.3 - - + -
90B ALA 3.0 16.9 + - - +
91B LEU* 2.9 28.2 + - + +
93B SER* 1.3 77.5 - - - +
95B ILE* 1.3 71.2 + - + +
97B GLY* 3.4 2.3 + - - -
98B PHE* 3.3 45.1 + - + -
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Residues in contact with ILE 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 2.8 26.8 + - + +
94B MET* 1.3 82.0 - - + +
96B TYR* 1.3 62.7 - - - +
97B GLY 3.0 5.8 + - - -
98B PHE* 3.3 15.4 + - + +
99B PHE* 3.2 39.3 - - + -
113B SER* 4.4 1.3 - - - +
116B CYS* 4.1 9.4 - - + +
117B VAL* 3.8 27.8 - - + -
120B ILE* 4.1 28.5 - - + -
121B CYS* 4.3 18.6 - - - -
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Residues in contact with TYR 96 (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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45B PHE* 4.7 4.3 - - + +
48B SER* 4.0 13.5 - - - -
49B VAL* 3.5 43.9 - - + +
52B GLY* 4.1 7.1 - - - +
92B GLU* 3.0 28.5 + - + +
93B SER 4.3 4.3 - - - +
94B MET 3.5 0.2 - - - -
95B ILE* 1.3 76.5 - - - +
97B GLY* 1.3 56.7 + - - +
99B PHE* 4.7 1.3 - - - -
100B LEU* 2.9 57.3 + - + +
113B SER* 3.8 17.0 - - - -
114B VAL* 4.0 23.6 - - + +
117B VAL* 3.4 36.0 - - + +
122B TYR* 4.4 3.5 + - - -
156B HIS* 4.4 13.9 + - - -
160B VAL* 4.3 5.3 - - + +
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Residues in contact with GLY 97 (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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52B GLY* 3.5 20.4 - - - -
57B PRO* 4.2 16.6 - - - -
93B SER 3.5 7.0 + - - -
94B MET 3.4 7.1 + - - -
95B ILE 3.0 1.6 - - - -
96B TYR* 1.3 74.9 - - - +
98B PHE* 1.3 58.1 + - - -
99B PHE 2.9 10.3 + - - -
101B TYR* 3.1 29.7 + - - +
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Residues in contact with PHE 98 (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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57B PRO* 3.5 31.0 - - + -
58B TRP* 4.1 25.8 - + - -
94B MET* 3.3 34.8 + - + -
95B ILE* 3.3 12.8 + - + +
97B GLY* 1.3 72.0 - - - +
99B PHE* 1.3 67.1 + - + +
103B LYS* 4.6 10.8 - - - -
109B ARG* 5.4 0.7 + - - -
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Residues in contact with PHE 99 (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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95B ILE* 3.2 38.7 + - + +
96B TYR 4.2 0.4 - - - +
97B GLY 2.9 1.2 + - - -
98B PHE* 1.3 87.5 - - + +
100B LEU* 1.3 61.1 + - + +
101B TYR 3.6 0.7 - - - -
103B LYS* 3.4 25.1 - - - +
108B TRP* 4.7 14.4 - + - -
109B ARG* 3.4 22.1 + - + +
112B ALA* 3.6 26.2 - - + -
113B SER* 3.7 24.7 - - - -
116B CYS* 3.5 34.3 - - + -
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 4.3 9.4 - - + +
52B GLY 4.8 0.4 - - - -
53B TYR* 3.3 31.8 - - + -
96B TYR* 2.9 60.2 + - + +
99B PHE* 1.3 77.6 - - + +
101B TYR* 1.3 61.4 + - - +
102B LYS 3.5 1.6 + - - -
103B LYS* 4.0 9.7 + - - +
109B ARG* 4.9 13.7 - - + +
110B VAL* 4.6 14.8 - - + -
113B SER* 3.9 12.3 - - - +
160B VAL* 4.6 2.7 - - + -
164B LEU* 3.4 37.3 - - + +
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Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLY 3.6 9.9 - - - +
53B TYR 3.2 17.7 - - - -
54B LEU 3.5 22.0 + - - -
55B PHE* 4.3 4.4 + - - -
56B GLY* 3.5 25.1 - - - -
57B PRO* 4.2 9.2 - - + -
96B TYR 4.2 0.2 + - - -
97B GLY 3.1 20.2 + - - +
99B PHE 3.6 1.6 - - - -
100B LEU* 1.3 73.5 - - - +
102B LYS* 1.3 108.8 + - + +
103B LYS* 3.5 13.7 + - - +
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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