Contacts of the helix formed by residues 81 - 92 (chain B) in PDB entry 2IWI
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 PRO 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B ILE* 5.4 7.0 - - + -
80B CYS* 1.3 94.9 - - + +
82B LEU* 1.3 66.6 + - - +
83B GLU* 4.3 9.6 - - + +
84B VAL* 3.0 29.7 + - + +
85B ALA 3.2 8.5 + - - -
105B TRP* 4.4 4.0 - - + -
112B PHE* 3.8 46.6 - - + -
114B LEU* 5.3 4.3 - - + -
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Residues in contact with LEU 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 CYS 3.6 2.7 + - - -
81B PRO* 1.3 70.2 - - - +
83B GLU* 1.3 58.1 + - - +
85B ALA* 2.9 13.2 + - + +
86B LEU* 2.8 50.4 + - + +
186B GLY 4.4 9.9 - - - +
187B ALA* 5.0 4.9 - - + -
188B LEU* 5.7 7.0 - - + +
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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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43B PHE 5.8 0.2 - - - +
61B LYS* 5.4 5.7 - - - +
63B ILE* 3.5 21.1 - - + +
81B PRO* 3.2 7.3 - - + +
82B LEU* 1.3 79.0 - - - +
84B VAL* 1.3 57.0 + - - +
86B LEU* 3.4 5.6 + - - +
87B LEU* 3.0 35.8 + - + +
114B LEU* 4.0 22.9 - - + +
116B LEU* 5.6 2.6 - - - +
182B ASP* 3.8 8.4 - - - +
183B PHE* 3.2 42.6 + - + +
184B GLY* 3.4 24.9 + - - +
1288B HB1 5.8 0.9 - - - -
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B CYS* 3.9 15.0 - - + -
81B PRO* 3.0 23.6 + - + +
83B GLU* 1.3 73.6 - - - +
85B ALA* 1.3 68.9 + - - +
87B LEU* 3.1 2.6 + - - +
88B TRP* 2.9 27.0 + - + +
102B LEU* 3.7 25.0 - - + +
105B TRP* 3.5 50.0 - - + +
114B LEU* 4.1 14.4 - - + -
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B CYS* 3.8 12.5 - - - -
81B PRO 3.2 6.0 + - - +
82B LEU* 2.9 16.3 + - + +
84B VAL* 1.3 81.2 - - - +
86B LEU* 1.3 64.3 + - + +
88B TRP* 3.4 5.6 + - - +
89B LYS* 3.2 30.6 + - + +
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Residues in contact with LEU 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 LEU* 2.8 29.4 + - + +
83B GLU* 3.7 4.7 - - - +
85B ALA* 1.3 77.1 - - + +
87B LEU* 1.3 65.8 + - - +
89B LYS* 3.2 5.2 + - + +
90B VAL* 2.9 28.6 + - - +
159B VAL* 3.4 38.8 - - + -
183B PHE* 3.9 23.1 - - + +
186B GLY* 3.6 34.8 - - - +
187B ALA* 3.8 15.7 - - - +
188B LEU* 4.2 17.3 - - + +
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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
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83B GLU* 3.0 39.8 + - + +
84B VAL 3.8 3.1 - - - +
86B LEU* 1.3 75.8 - - - +
88B TRP* 1.3 53.1 + - - +
90B VAL* 3.6 3.6 - - + +
91B GLY* 2.7 32.7 + - - -
99B VAL* 4.8 2.9 - - + -
100B ILE* 3.6 23.6 - - + +
101B ARG* 5.9 0.2 - - - -
102B LEU* 3.9 30.3 + - + +
114B LEU* 4.6 3.1 - - + -
116B LEU* 3.7 27.6 - - + -
183B PHE* 3.5 36.8 - - + -
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Residues in contact with TRP 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 VAL* 2.9 21.4 + - + +
85B ALA* 3.8 6.1 - - - +
87B LEU* 1.3 72.9 - - - +
89B LYS* 1.3 65.8 + - + +
91B GLY* 3.6 2.4 - - - +
92B ALA* 3.0 24.3 + - - +
102B LEU* 5.3 3.0 - - + +
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Residues in contact with LYS 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 ALA* 3.2 17.9 + - + +
86B LEU* 3.2 7.5 + - + +
88B TRP* 1.3 80.9 - - + +
90B VAL* 1.3 59.8 + - - +
92B ALA* 3.5 8.5 + - - +
157B ARG* 3.1 55.5 + - + +
158B GLY* 3.3 17.4 + - - -
159B VAL* 3.8 11.0 - - + +
188B LEU* 3.3 33.7 - - + +
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Residues in contact with VAL 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 LEU 2.9 18.5 + - - +
87B LEU* 3.8 6.3 - - + +
89B LYS* 1.3 77.6 - - - +
91B GLY* 1.3 59.5 + - - +
92B ALA 3.5 2.1 + - - +
95B GLY* 4.2 4.7 - - - -
99B VAL* 3.4 32.3 - - + -
153B HIS* 2.7 48.6 + - + +
154B CYS* 3.9 13.5 - - + -
157B ARG* 3.9 4.3 - - + -
159B VAL* 3.8 30.3 - - + -
183B PHE* 4.3 9.9 - - + -
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Residues in contact with GLY 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 LEU 2.7 21.1 + - - -
88B TRP* 3.6 3.6 - - - -
90B VAL* 1.3 70.2 - - - +
92B ALA* 1.3 66.1 + - - +
93B GLY 3.5 3.8 + - - +
94B GLY* 3.9 8.7 + - - -
95B GLY* 4.7 8.0 + - - -
99B VAL* 6.1 1.1 - - - -
101B ARG* 5.5 13.2 - - - -
102B LEU 6.0 0.4 - - - -
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TRP 3.0 11.8 + - - +
89B LYS* 3.5 16.6 - - - +
90B VAL 3.3 1.5 - - - +
91B GLY* 1.3 76.8 - - - +
93B GLY* 1.3 51.4 + - - +
94B GLY 2.7 17.2 + - - +
157B ARG* 2.7 31.2 + - - +
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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