Contacts of the helix formed by residues 75 - 89 (chain B) in PDB entry 2BEW
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 CYS 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLY 5.4 0.7 - - - -
202A HIS* 5.6 6.7 - - - -
203A ALA* 3.6 26.7 - - - -
207A PHE* 3.7 16.7 - - + -
46B GLU* 3.4 4.8 + - - -
73B PRO* 3.0 8.8 + - + -
74B LEU* 1.3 76.5 - - - +
76B GLU* 1.3 63.8 + - - +
77B GLN* 3.8 15.3 - - - -
78B GLY* 3.1 16.2 + - - -
79B ILE* 3.0 28.1 + - - +
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Residues in contact with GLU 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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46B GLU* 2.7 29.9 - - - +
74B LEU* 4.3 8.5 - - - +
75B CYS* 1.3 73.2 - - - +
77B GLN* 1.3 67.6 + - - +
79B ILE* 3.7 9.5 - - + +
80B VAL* 3.1 20.6 + - - +
97B ILE* 3.7 22.9 - - + -
98B GLN* 5.4 2.6 + - - +
102B TYR* 3.2 39.7 - - - +
105B PRO* 4.0 21.0 - - + +
106B ALA* 3.5 13.4 - - + +
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Residues in contact with GLN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PRO* 4.4 1.7 - - - +
199A GLY* 3.4 15.7 - - - -
200A ASP* 3.0 46.6 + - - +
203A ALA* 4.2 4.9 - - + -
75B CYS* 3.8 16.4 - - - -
76B GLU* 1.3 78.6 - - - +
78B GLY* 1.3 59.6 + - - +
80B VAL* 4.2 0.2 - - - -
81B GLY* 3.1 22.5 + - - -
105B PRO* 3.5 33.7 + - - +
106B ALA* 4.1 7.0 - - - +
109B GLN* 3.8 13.2 - - + +
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Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PRO* 4.2 7.4 - - - +
203A ALA* 3.7 21.8 - - - -
207A PHE* 3.6 14.5 - - - -
75B CYS* 3.1 8.6 + - - -
76B GLU 3.0 0.2 - - - -
77B GLN* 1.3 84.1 - - - +
79B ILE* 1.3 58.6 + - - +
82B PHE* 2.8 34.3 + - - +
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Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A PHE* 3.6 8.9 - - + -
44B PHE* 3.6 19.9 - - + +
45B GLY* 4.1 5.8 - - - -
46B GLU* 3.7 26.5 - - + +
72B THR* 3.5 28.0 - - - +
73B PRO 4.5 0.4 - - - +
75B CYS 3.0 18.2 + - - +
76B GLU* 3.2 11.9 + - + +
78B GLY* 1.3 75.4 - - - +
80B VAL* 1.3 59.5 + - - +
82B PHE* 3.7 0.8 - - - +
83B GLY* 3.0 21.7 + - - -
95B ALA* 3.9 19.6 - - + +
96B GLU 3.9 25.1 - - - +
97B ILE* 4.3 11.9 - - + -
98B GLN 6.2 0.2 - - - +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU 3.1 6.1 + - - +
77B GLN 4.4 0.2 - - - +
79B ILE* 1.3 76.7 - - + +
81B GLY* 1.3 66.4 + - - +
83B GLY* 3.2 2.1 + - - -
84B ILE* 2.9 34.7 + - + +
95B ALA* 5.4 0.7 - - + -
97B ILE* 4.2 16.6 - - + -
106B ALA* 3.5 29.2 - - + -
109B GLN* 3.8 19.5 - - + -
110B ILE* 3.9 20.0 - - + -
130B LEU* 4.7 4.8 - - + +
132B ILE* 4.1 27.8 - - + -
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Residues in contact with GLY 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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169A PRO* 3.8 11.9 - - - -
170A GLN* 3.2 15.5 - - - +
77B GLN 3.1 14.9 + - - -
78B GLY 3.9 0.2 - - - -
80B VAL* 1.3 77.5 - - - +
82B PHE* 1.3 61.4 + - - +
84B ILE* 3.3 0.8 + - - -
85B GLY 3.1 17.3 + - - -
109B GLN* 3.5 30.1 + - - -
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Residues in contact with PHE 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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169A PRO* 3.4 13.5 + - + +
172A VAL* 3.9 16.8 - - + -
173A GLY* 3.4 32.3 - - - -
176A TYR* 3.7 31.4 - + + -
207A PHE* 4.0 20.0 - + + -
211A LEU* 3.6 24.2 - - + -
213A CYS* 4.7 0.7 - - - -
44B PHE* 3.8 19.1 - + - -
70B PHE* 3.7 20.9 - + - -
72B THR* 5.0 0.4 - - + -
78B GLY 2.8 22.3 + - - +
79B ILE 3.7 2.2 - - - +
81B GLY* 1.3 70.9 - - - +
83B GLY* 1.3 58.4 + - - +
85B GLY 3.1 1.9 + - - -
86B ILE* 3.0 44.3 + - + +
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Residues in contact with GLY 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE* 3.6 25.4 - - - -
79B ILE 3.0 13.1 + - - -
80B VAL 3.2 2.9 + - - -
82B PHE* 1.3 75.3 - - - +
84B ILE* 1.3 65.2 + - - +
86B ILE* 3.3 2.0 + - - -
87B ALA* 3.0 22.5 + - - +
93B ALA* 3.6 8.4 - - - +
130B LEU* 3.9 14.7 - - - +
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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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170A GLN* 3.8 9.0 - - + -
80B VAL* 2.9 26.1 + - + +
81B GLY 3.5 6.1 - - - +
83B GLY* 1.3 70.5 - - - +
85B GLY* 1.3 58.9 + - - +
87B ALA* 3.1 4.5 + - - +
88B VAL* 2.8 31.1 + - + +
109B GLN* 3.4 43.7 - - - +
113B GLU* 4.1 2.9 - - + -
114B ALA* 3.8 18.2 - - + +
117B TYR* 3.5 37.0 - - + -
127B CYS* 4.0 14.7 - - + +
130B LEU* 3.7 19.8 - - + +
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Residues in contact with GLY 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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110A PHE* 5.1 0.7 - - - -
170A GLN* 3.2 30.7 - - - +
174A ALA* 3.5 21.2 - - - +
81B GLY 3.1 11.9 + - - -
82B PHE 3.1 2.2 + - - -
84B ILE* 1.3 76.3 - - - +
86B ILE* 1.3 65.3 + - - +
88B VAL* 3.3 16.5 + - - +
89B THR* 3.6 5.9 + - - +
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLY* 3.3 21.9 - - - +
176A TYR* 4.5 6.7 - - + -
177A ALA* 4.4 10.1 - - + +
42B VAL* 3.9 24.2 - - + -
44B PHE* 3.9 9.4 - - + -
82B PHE* 3.0 45.1 + - + +
83B GLY 3.7 7.2 - - - +
84B ILE 3.3 0.2 - - - -
85B GLY* 1.3 75.8 - - - +
87B ALA* 1.3 62.2 + - - +
89B THR* 2.7 25.5 + - - -
91B ALA* 3.4 27.6 + - + +
92B THR 4.4 2.2 - - - +
93B ALA* 3.8 15.9 - - + -
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Residues in contact with ALA 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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83B GLY 3.0 13.7 + - - +
84B ILE 3.5 7.6 - - - +
86B ILE* 1.3 75.9 - - - +
88B VAL* 1.3 66.9 + - - +
90B GLY* 2.9 12.6 + - - -
91B ALA 3.4 3.4 - - - +
93B ALA* 4.7 0.7 - - + -
126B ASN* 3.6 10.4 - - - +
127B CYS* 3.7 21.9 - - + -
129B SER* 3.3 26.6 + - - +
130B LEU* 3.8 16.6 - - + +
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 5.1 2.5 - - + -
110A PHE* 4.4 17.9 - - + -
158A VAL* 4.5 5.2 - - + -
84B ILE* 2.8 26.7 + - + +
85B GLY* 3.6 12.1 - - - +
86B ILE 3.2 0.2 - - - -
87B ALA* 1.3 74.2 - - - +
89B THR* 1.3 59.1 + - + +
90B GLY* 3.5 0.5 + - - -
117B TYR* 3.5 37.7 - - + +
125B PHE* 4.3 18.5 - - + -
126B ASN 3.3 16.7 + - - +
1346B GOL 3.2 28.4 + - - +
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Residues in contact with THR 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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108A LEU* 4.9 2.0 - - + -
174A ALA* 3.7 28.9 - - + +
177A ALA* 3.4 21.0 - - + +
178A ALA* 5.3 0.7 - - + +
185A ARG* 4.9 5.2 - - - +
85B GLY 3.6 14.1 - - - +
86B ILE 2.7 16.0 + - - -
87B ALA 3.1 0.2 - - - -
88B VAL* 1.3 76.9 - - - +
90B GLY* 1.3 56.8 + - - +
91B ALA* 3.6 7.3 + - - +
1346B GOL 3.9 28.3 + - - +
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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
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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