Contacts of the helix formed by residues 90 - 106 (chain B) in PDB entry 5I1U
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 ARG 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B GLY 4.1 0.4 + - - -
89B ARG* 1.3 72.8 - - - +
91B PRO* 1.3 73.0 - - + +
92B GLU* 3.0 34.0 + - - +
93B GLN* 2.8 62.0 + - + +
94B VAL* 3.0 10.7 + - - +
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Residues in contact with PRO 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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278A SER 3.5 17.0 - - - +
279A MET* 3.8 23.8 - - + -
280A SER* 5.7 0.9 - - - +
89B ARG 3.5 5.4 - - - +
90B ARG* 1.3 83.1 - - - +
92B GLU* 1.3 63.3 + - - +
94B VAL* 3.3 4.2 + - + +
95B ALA* 2.8 28.6 + - - +
151B PRO* 3.8 19.2 - - - +
154B ALA* 4.1 10.8 - - + +
155B ALA* 3.7 25.1 - - - +
158B THR* 5.8 5.6 - - + -
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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
----------------------------------------------------------
196A HIS* 5.8 0.2 - - - -
279A MET 3.6 15.2 + - - +
280A SER* 3.6 33.4 + - - +
90B ARG* 3.0 50.1 + - - +
91B PRO* 1.3 86.5 - - - +
93B GLN* 1.3 60.2 + - + +
95B ALA* 3.4 9.5 + - + +
96B LEU* 3.2 20.6 + - - +
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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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89B ARG* 5.1 13.1 + - + -
90B ARG* 2.8 67.8 + - + +
92B GLU* 1.3 75.2 - - + +
94B VAL* 1.3 65.2 + - + +
96B LEU* 3.3 10.1 + - - +
97B ILE* 3.2 31.3 + - + +
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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
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83B PHE* 3.8 27.6 - - + -
89B ARG* 3.7 24.2 - - + -
90B ARG 3.0 13.7 + - - +
91B PRO* 3.3 9.4 + - + +
93B GLN* 1.3 76.1 - - - +
95B ALA* 1.3 57.3 + - - +
97B ILE* 3.3 8.1 + - + +
98B CYS* 2.9 30.2 + - - +
150B HIS* 3.7 33.2 - - + +
151B PRO* 3.7 11.2 - - + -
154B ALA* 4.0 15.3 - - + -
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Residues in contact with ALA 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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195A GLN* 4.8 1.4 + - - +
196A HIS* 3.5 43.7 + - + +
91B PRO 2.8 16.8 + - - +
92B GLU* 3.5 10.5 - - - +
93B GLN 3.1 0.4 - - - -
94B VAL* 1.3 78.1 - - - +
96B LEU* 1.3 57.6 + - - +
98B CYS* 3.4 1.6 + - - +
99B GLU* 2.9 33.3 + - - +
151B PRO* 3.4 10.1 - - + -
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Residues in contact with LEU 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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92B GLU 3.2 12.3 + - - +
93B GLN* 3.5 11.7 - - - +
95B ALA* 1.3 74.3 - - - +
97B ILE* 1.3 66.1 + - + +
99B GLU* 3.4 8.2 + - + +
100B ARG* 3.2 40.2 + - + +
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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
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79B PHE* 4.4 1.3 - - + -
82B GLN* 4.1 23.1 - - - +
83B PHE* 4.1 29.8 - - + -
89B ARG* 6.1 4.7 - - - -
93B GLN* 3.2 19.8 + - + +
94B VAL* 3.6 7.0 - - + +
96B LEU* 1.3 80.7 - - + +
98B CYS* 1.3 64.7 + - - +
100B ARG* 3.4 9.3 + - - +
101B LEU* 3.3 38.0 + - + +
116B SER* 5.9 1.3 - - - -
117B GLU* 4.8 2.4 - - - +
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Residues in contact with CYS 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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195A GLN* 3.2 12.8 + - - +
79B PHE* 4.3 18.2 - - - -
83B PHE* 4.4 4.0 - - - -
94B VAL* 2.9 24.8 + - - +
95B ALA* 4.0 3.8 - - - +
97B ILE* 1.3 75.8 - - - +
99B GLU* 1.3 61.0 + - - +
101B LEU* 3.3 5.3 + - - -
102B SER* 3.0 26.0 + - - -
147B PHE* 3.3 35.6 - - + +
150B HIS* 3.6 23.8 - - - -
151B PRO* 4.6 2.7 - - + -
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Residues in contact with GLU 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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134A ARG* 2.9 39.5 + - - -
195A GLN* 3.4 20.8 + - + +
196A HIS* 6.2 1.1 - - + +
95B ALA 2.9 19.2 + - - +
96B LEU* 3.8 9.6 - - + +
97B ILE 3.3 0.2 - - - -
98B CYS* 1.3 78.1 - - - +
100B ARG* 1.3 59.7 + - + +
102B SER* 3.3 2.1 + - - -
103B ALA* 3.0 28.3 + - + +
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Residues in contact with ARG 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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96B LEU* 3.2 27.6 + - + +
97B ILE* 3.7 8.3 - - - +
99B GLU* 1.3 80.7 - - + +
101B LEU* 1.3 62.0 + - - +
103B ALA* 3.3 5.4 + - - +
104B ILE* 3.3 23.3 + - - +
109B LEU* 3.6 27.0 - - + +
110B THR* 6.1 1.8 - - - -
111B ALA 3.1 21.6 + - - +
113B THR* 4.0 10.9 + - - -
117B GLU* 2.7 48.0 + - - +
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Residues in contact with LEU 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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75B PHE* 4.8 1.3 - - + -
79B PHE* 3.4 37.2 - - + -
97B ILE* 3.3 27.3 + - + +
98B CYS* 3.8 5.6 - - - +
99B GLU 3.3 0.2 - - - -
100B ARG* 1.3 76.3 - - - +
102B SER* 1.3 65.6 + - - +
104B ILE* 3.1 17.5 + - + +
105B ALA 3.4 7.4 + - - -
116B SER* 4.0 17.7 - - - +
117B GLU* 4.1 19.5 - - + -
120B PHE* 3.7 40.4 - - + -
147B PHE* 3.7 22.9 - - + -
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Residues in contact with SER 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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134A ARG* 3.7 14.1 - - - -
195A GLN* 2.7 30.6 + - - -
98B CYS 3.0 12.4 + - - -
99B GLU 3.7 4.9 - - - -
101B LEU* 1.3 76.3 - - - +
103B ALA* 1.3 61.7 + - - +
105B ALA* 3.1 15.7 + - - +
106B HIS* 3.1 21.0 + - - -
144B GLU* 3.5 23.0 - - - +
147B PHE* 3.6 12.2 - - - +
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Residues in contact with ALA 103 (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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134A ARG* 4.4 9.1 - - - +
99B GLU* 3.0 16.1 + - + +
100B ARG* 3.4 11.9 - - - +
101B LEU 3.1 0.2 - - - -
102B SER* 1.3 77.8 - - - +
104B ILE* 1.3 55.0 + - - +
106B HIS* 3.3 1.4 + - - +
107B GLY 2.9 7.4 + - - -
108B THR* 2.7 48.7 + - - +
109B LEU* 3.8 21.5 - - + +
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Residues in contact with ILE 104 (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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100B ARG 3.3 6.3 + - - +
101B LEU* 3.1 10.2 + - + +
103B ALA* 1.3 78.9 - - - +
105B ALA* 1.3 61.8 + - - +
107B GLY* 3.0 13.6 + - - -
108B THR 4.9 0.2 - - - +
109B LEU* 3.3 38.1 - - + +
112B VAL* 4.6 8.1 - - + -
117B GLU* 3.9 37.0 - - + +
120B PHE* 3.6 24.5 - - + -
121B ALA* 4.0 21.1 - - + -
124B TRP* 3.6 15.2 - - + -
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Residues in contact with ALA 105 (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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101B LEU 3.4 4.0 + - - +
102B SER* 3.1 11.8 + - - +
104B ILE* 1.3 78.6 - - - +
106B HIS* 1.3 60.7 + - + +
107B GLY 3.3 0.2 - - - -
120B PHE* 3.9 19.9 - - + -
124B TRP* 3.1 37.3 + - + +
140B ALA* 3.7 20.5 - - + +
143B TRP* 4.1 18.2 - - + -
144B GLU 5.3 0.4 - - - +
147B PHE* 5.2 0.2 - - + -
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Residues in contact with HIS 106 (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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133A ASP* 6.1 1.4 - - - +
134A ARG* 3.5 58.5 - - + +
137A ALA* 4.1 14.1 - - + +
102B SER 3.1 22.3 + - - +
103B ALA 3.3 2.9 + - - +
105B ALA* 1.3 77.8 - - + +
107B GLY* 1.3 62.4 + - - +
108B THR* 3.3 15.0 + - + +
140B ALA* 3.7 33.6 + - + +
141B CYS* 4.2 4.0 - - - -
144B GLU* 2.8 30.4 + - + -
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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