Contacts of the helix formed by residues 85 - 102 (chain B) in PDB entry 3CWR
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 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B PRO* 4.1 4.1 - - - +
84B GLN* 1.3 78.6 - - + +
86B ALA* 1.3 62.3 + - - +
87B ALA* 3.3 11.1 + - - +
88B ALA* 3.1 32.4 + - + +
89B ALA* 3.1 21.3 + - - +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PRO* 4.0 13.2 - - + +
84B GLN 3.8 3.8 + - - -
85B ASP* 1.3 70.7 + - - +
87B ALA* 1.3 59.0 + - - +
89B ALA 3.3 0.5 + - - -
90B LEU* 2.9 28.6 + - - +
142B TRP* 3.4 6.7 - - + -
146B GLN* 4.3 10.3 - - - +
151B ARG* 3.7 28.6 - - + +
152B LEU* 3.3 31.4 - - + -
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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
----------------------------------------------------------
85B ASP* 3.2 8.8 + - - +
86B ALA* 1.3 78.4 - - - +
88B ALA* 1.3 64.1 + - - +
90B LEU* 3.2 8.5 + - - +
91B GLU* 3.0 30.1 + - - +
152B LEU* 4.5 13.3 - - + +
198B VAL* 4.1 18.4 - - + +
202B ALA 5.0 1.3 - - - +
203B PRO* 5.2 6.3 - - + -
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASP* 3.1 34.1 + - + +
87B ALA* 1.3 76.4 - - - +
89B ALA* 1.3 62.6 + - - +
91B GLU* 3.3 14.8 + - - +
92B ARG* 3.1 20.6 + - - +
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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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80B GLU* 5.4 3.6 - - + +
83B PRO* 3.9 17.5 - - + -
85B ASP 3.1 12.6 + - - +
86B ALA 3.6 7.6 - - - +
87B ALA 3.2 0.2 - - - -
88B ALA* 1.3 73.1 - - - +
90B LEU* 1.3 66.3 + - - +
92B ARG* 3.2 7.8 + - - +
93B ILE* 3.0 27.6 + - + +
142B TRP* 3.8 20.0 - - + -
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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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86B ALA 2.9 17.1 + - - +
87B ALA* 3.2 6.5 + - - +
89B ALA* 1.3 78.2 - - - +
91B GLU* 1.3 61.1 - - - +
93B ILE* 3.2 3.2 + - + -
94B VAL* 2.9 39.8 + - + +
139B LEU* 3.7 30.3 - - + -
142B TRP* 3.9 15.5 - - + -
143B LEU* 4.0 13.9 - - + -
152B LEU* 4.3 8.1 - - + -
165B LEU* 3.8 24.0 - - + -
198B VAL* 4.1 15.3 - - + -
202B ALA* 3.9 22.2 - - + +
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Residues in contact with GLU 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 ALA* 3.0 22.5 + - - +
88B ALA* 3.6 11.9 - - - +
89B ALA 3.3 0.2 - - - -
90B LEU* 1.3 77.9 - - - +
92B ARG* 1.3 61.3 + - - +
95B TYR* 3.0 25.6 + - - +
191B ALA 5.0 1.2 - - - +
194B VAL* 3.4 18.3 - - + +
195B ALA* 3.6 34.5 + - - +
198B VAL* 3.9 22.8 - - + +
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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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88B ALA 3.1 12.9 + - - +
89B ALA* 3.6 9.9 - - - +
90B LEU 3.2 0.2 - - - -
91B GLU* 1.3 77.9 - - - +
93B ILE* 1.3 61.6 + - + +
95B TYR* 3.5 28.2 + - - +
96B ASP* 2.9 54.4 + - - +
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Residues in contact with ILE 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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75B ILE* 4.4 7.3 - - + +
76B PHE* 3.6 39.0 - - + -
89B ALA* 3.0 19.4 + - + +
90B LEU* 3.2 6.9 + - - +
92B ARG* 1.3 77.9 - - + +
94B VAL* 1.3 60.1 + - - +
96B ASP* 3.2 8.5 + - - +
97B ILE* 3.0 38.5 + - + +
139B LEU* 3.9 12.1 - - + -
142B TRP* 3.8 44.6 - - + +
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU* 2.9 39.1 + - + +
93B ILE* 1.3 74.2 - - + +
95B TYR* 1.3 60.6 + - - +
97B ILE* 3.2 6.9 + - - +
98B ALA* 2.9 28.2 + - - +
139B LEU* 4.5 4.5 - - + -
165B LEU* 4.0 19.1 - - + -
166B LEU* 4.2 21.3 - - + -
169B VAL* 3.9 37.2 - - + -
170B ILE* 4.9 0.8 - - + +
194B VAL* 4.1 12.6 - - + -
198B VAL* 5.2 1.1 - - + -
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Residues in contact with TYR 95 (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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91B GLU 3.0 20.0 + - - +
92B ARG* 3.5 35.9 - - - +
94B VAL* 1.3 76.5 - - - +
96B ASP* 1.3 59.8 + - - +
98B ALA* 3.3 4.6 + - - +
99B GLN* 2.9 66.2 + - + +
186B PRO* 5.9 1.2 - - - +
189B ASP* 4.8 3.8 + - - -
190B ILE* 3.8 18.4 - - + -
191B ALA* 4.1 28.3 - - + -
194B VAL* 4.1 11.5 - - + +
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Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ILE* 4.1 22.9 - - + +
92B ARG* 2.9 58.5 + - - +
93B ILE* 3.2 6.3 + - - +
95B TYR* 1.3 80.0 - - - +
97B ILE* 1.3 62.3 + - - +
99B GLN* 3.3 6.6 + - - +
100B ALA* 3.1 23.0 + - - +
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ILE* 3.8 26.2 - - + -
76B PHE* 4.2 9.6 - - + -
93B ILE* 3.0 36.2 + - + +
94B VAL 3.7 6.1 - - - +
96B ASP* 1.3 73.9 - - - +
98B ALA* 1.3 65.0 + - - +
100B ALA* 3.0 12.6 + - - +
101B VAL* 3.0 17.4 + - + +
132B ILE* 3.8 20.6 - - + -
135B SER* 4.2 23.6 - - - +
139B LEU* 4.8 2.9 - - + -
166B LEU* 3.9 22.2 - - + -
170B ILE* 3.8 18.8 - - + -
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Residues in contact with ALA 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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94B VAL 2.9 17.2 + - - +
95B TYR* 3.6 5.8 - - - +
97B ILE* 1.3 77.9 - - - +
99B GLN* 1.3 62.8 + - - +
101B VAL* 3.3 1.5 + - - -
102B LEU* 2.9 31.0 + - + +
169B VAL* 4.5 3.8 - - + -
170B ILE* 3.9 26.9 - - + +
185B LEU* 4.0 4.3 - - + -
190B ILE* 4.0 27.1 - - + -
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Residues in contact with GLN 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 TYR* 2.9 65.0 + - + +
96B ASP* 3.7 8.3 - - - +
97B ILE 3.3 0.4 - - - -
98B ALA* 1.3 76.6 - - - +
100B ALA* 1.3 60.7 + - - +
102B LEU 4.3 0.2 - - - -
103B SER* 3.6 22.3 + - - -
185B LEU* 3.5 26.9 - - - +
186B PRO* 3.7 19.2 - - - +
188B TRP 5.4 1.0 + - - -
190B ILE* 3.7 17.4 - - - +
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Residues in contact with ALA 100 (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 TRP* 3.5 42.5 - - + +
72B ILE* 4.5 0.4 - - + -
75B ILE* 4.0 11.0 - - + -
96B ASP 3.1 12.3 + - - +
97B ILE 3.0 9.9 + - - +
99B GLN* 1.3 79.7 - - - +
101B VAL* 1.3 64.2 + - + +
103B SER* 3.9 5.3 + - - -
106B ALA* 3.6 14.0 - - - +
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Residues in contact with VAL 101 (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 TRP* 5.6 4.7 - - + -
72B ILE* 4.2 22.9 - - + -
97B ILE* 3.0 21.3 + - + +
98B ALA 4.1 2.2 - - - +
100B ALA* 1.3 80.6 - - - +
102B LEU* 1.3 63.7 + - - +
106B ALA* 3.3 21.4 - - + +
107B VAL* 4.2 5.2 - - - +
131B GLY* 6.1 0.7 - - - -
132B ILE* 4.6 23.8 - - + +
170B ILE* 3.7 38.6 - - + -
174B LEU* 4.6 4.7 - - - +
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Residues in contact with LEU 102 (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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98B ALA* 2.9 17.3 + - + +
99B GLN 4.3 0.2 - - - -
101B VAL* 1.3 87.6 - - - +
103B SER* 1.3 63.2 + - - +
107B VAL* 3.9 6.9 - - - +
170B ILE* 3.8 23.8 - - + +
173B PRO* 3.8 22.0 - - + -
174B LEU* 3.6 42.4 - - + +
177B ILE* 4.0 9.6 - - + +
184B PRO* 3.6 5.4 - - - +
185B LEU* 3.0 50.0 + - + -
190B ILE* 3.9 12.8 - - + -
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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
------------------------------------------------------------
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