Contacts of the helix formed by residues 87 - 100 (chain B) in PDB entry 2I2R
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 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ARG* 3.0 29.2 + - - -
96A ASN* 3.0 42.0 + - - +
46B VAL* 3.8 1.6 - - - +
86B ARG* 1.3 77.8 - - - +
88B PRO* 1.3 68.3 - - - +
89B GLU* 3.1 5.2 + - - +
90B VAL* 2.5 42.7 + - + +
91B PHE* 3.7 15.8 + - - +
109B GLU* 4.6 0.7 - - - -
117B GLU* 4.1 18.4 + - + +
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Residues in contact with PRO 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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49A ARG* 4.2 18.2 - - - +
51A PHE* 5.0 2.5 - - + -
92A ARG* 4.3 14.8 - - + -
96A ASN* 4.2 6.3 - - - +
99A ARG* 4.6 1.6 - - - +
46B VAL* 3.5 28.9 - - + +
47B SER* 3.6 18.2 - - - +
49B ARG* 3.8 23.3 - - + +
51B PHE* 3.5 15.1 - - + -
86B ARG 3.5 0.4 - - - +
87B ASP* 1.3 89.5 - - - +
89B GLU* 1.3 71.1 + - - +
91B PHE* 3.3 14.0 - - - +
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Residues in contact with GLU 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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92A ARG* 3.3 39.9 - - - +
49B ARG* 4.3 9.9 + - - +
87B ASP* 3.1 4.4 + - - +
88B PRO* 1.3 81.4 - - - +
90B VAL* 1.3 67.1 + - - +
92B ARG* 2.6 66.5 + - - +
93B CYS* 4.1 1.7 + - - -
108B TYR* 2.7 24.7 + - + +
109B GLU* 4.6 3.4 - - + +
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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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87B ASP* 2.5 18.4 + - - +
89B GLU* 1.3 73.5 - - - +
91B PHE* 1.3 54.8 + - - +
93B CYS* 2.7 33.5 + - - +
94B VAL* 3.3 17.2 + - + -
106B PRO* 5.7 0.9 - - + -
109B GLU* 3.5 27.1 - - + +
113B ALA* 4.7 3.1 - - + +
114B TYR* 3.9 40.8 - - + +
117B GLU* 3.4 37.9 - - + +
118B LEU* 5.3 0.7 - - + +
121B TYR* 5.1 0.2 - - + -
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Residues in contact with PHE 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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44B LEU* 3.5 27.1 - - + -
46B VAL* 3.6 25.6 - - + -
51B PHE* 4.0 24.5 - + + -
66B LEU* 3.8 14.8 - - + -
84B PHE* 4.3 7.2 - + - -
87B ASP 3.7 12.7 + - - +
88B PRO 3.3 13.0 - - - +
90B VAL* 1.3 79.4 - - - +
92B ARG* 1.3 55.6 + - - +
93B CYS 3.2 0.2 - - - -
94B VAL* 4.3 9.6 - - + -
95B LEU* 2.8 51.6 + - + +
121B TYR* 3.3 40.5 + + - +
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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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49B ARG* 5.0 5.6 - - - +
51B PHE* 4.2 23.5 - - + -
88B PRO 3.5 2.6 + - - -
89B GLU* 2.6 57.7 + - - +
91B PHE* 1.3 77.5 - - - +
93B CYS* 1.3 68.6 + - - +
95B LEU* 3.7 1.7 - - - +
96B ASN* 2.7 36.3 + - - +
106B PRO* 5.7 0.6 - - - +
108B TYR* 3.4 12.1 + - - -
87C ASP* 3.0 24.0 + - - +
88C PRO* 4.3 17.0 - - + -
89C GLU* 3.3 27.0 - - - +
108C TYR* 5.7 1.4 - - - -
109C GLU* 3.0 31.9 + - - -
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Residues in contact with CYS 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 GLU* 4.7 2.5 - - - -
90B VAL* 2.7 21.5 + - - +
92B ARG* 1.3 86.0 - - - +
94B VAL* 1.3 68.1 + - + +
96B ASN* 3.0 7.1 + - - +
97B PHE* 2.8 24.6 + - - +
103B LEU* 4.3 12.3 - - + +
104B HIS* 4.1 17.4 + - + +
106B PRO* 3.9 34.1 - - - -
108B TYR* 5.7 0.7 - - - -
114B TYR* 4.6 7.9 - - + -
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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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66B LEU* 4.2 7.6 - - + -
90B VAL* 3.3 17.2 + - + +
91B PHE* 3.7 12.1 - - + +
92B ARG 3.3 0.2 - - - -
93B CYS* 1.3 78.7 - - + +
95B LEU* 1.3 62.6 + - - +
97B PHE* 3.2 11.0 + - - +
98B TYR* 3.1 28.3 - - + -
103B LEU* 4.9 1.8 - - - -
114B TYR* 6.3 0.2 - - + -
118B LEU* 4.3 22.4 - - + -
121B TYR* 3.8 48.5 - - + -
123B ILE* 4.1 14.4 - - + -
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Residues in contact with LEU 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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44B LEU* 4.6 7.9 - - + -
51B PHE* 4.0 28.9 - - + -
52B GLN 4.6 0.2 - - - +
53B THR* 4.1 19.7 - - + +
58B LEU* 3.7 29.8 - - + -
66B LEU* 5.7 1.8 - - + -
91B PHE* 2.8 33.9 + - + +
92B ARG* 3.8 3.8 - - - +
94B VAL* 1.3 72.2 - - - +
96B ASN* 1.3 59.0 + - - +
98B TYR* 2.8 29.1 + - + +
99B ARG* 3.2 48.8 + - + +
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Residues in contact with ASN 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 ARG* 2.7 30.7 + - - +
93B CYS* 3.6 7.4 - - - +
95B LEU* 1.3 73.7 - - - +
97B PHE* 1.3 58.7 + - - +
98B TYR 3.3 0.2 - - - -
99B ARG* 3.6 21.5 - - - +
100B THR* 3.2 33.3 + - - +
102B LYS 4.2 2.5 - - - +
104B HIS* 5.9 5.6 - - + -
87C ASP* 2.8 58.0 + - - +
88C PRO* 4.1 3.2 - - - +
117C GLU* 4.7 3.6 - - - +
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Residues in contact with PHE 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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61B TYR* 3.4 51.8 - + + -
64B THR* 6.0 0.9 - - + -
93B CYS 2.8 14.6 + - - +
94B VAL* 3.4 9.6 - - - +
95B LEU 3.1 0.2 - - - -
96B ASN* 1.3 69.8 - - - +
98B TYR* 1.3 78.5 + + - +
99B ARG 3.1 0.2 - - - -
100B THR 2.5 17.3 - - - +
101B GLY 3.1 29.0 - - - +
102B LYS 3.4 10.7 + - - +
103B LEU* 3.3 37.0 - - + -
123B ILE* 4.3 20.2 - - + -
127B ILE* 3.9 36.8 - - + -
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Residues in contact with TYR 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 THR* 3.5 18.9 - - + +
58B LEU* 3.2 48.9 - - + -
60B ARG* 2.9 32.4 + - - -
61B TYR* 4.3 21.1 - + + -
64B THR* 2.5 32.0 + - + -
66B LEU* 3.5 27.7 + - + +
67B GLY* 3.5 16.1 + - - -
94B VAL* 3.1 32.5 - - + -
95B LEU* 2.8 12.4 + - + +
97B PHE* 1.3 88.7 - + - +
99B ARG* 1.3 59.3 + - - +
100B THR 4.4 0.3 - - - +
123B ILE* 4.1 5.4 - - + +
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Residues in contact with ARG 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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51B PHE* 5.6 1.4 - - - -
52B GLN 3.3 4.9 + - - -
53B THR* 4.1 0.4 + - - -
57B THR* 4.0 16.8 - - + -
60B ARG* 4.1 15.9 + - - +
92B ARG* 6.0 0.2 - - - +
95B LEU* 3.3 45.9 - - + +
96B ASN* 3.6 38.9 - - - +
97B PHE 3.1 2.0 - - - -
98B TYR* 1.3 80.7 - - - +
100B THR* 1.3 62.2 - - - +
101B GLY 4.1 0.3 + - - -
47C SER* 2.6 39.7 + - - -
85C ASP* 2.7 44.0 + - - +
86C ARG* 3.7 11.9 + - - +
87C ASP* 4.3 0.4 - - - +
88C PRO* 4.5 1.6 - - - +
62F ASN* 5.8 0.3 - - - +
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Residues in contact with THR 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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60B ARG* 6.3 0.2 - - - -
96B ASN* 3.2 14.3 + - - +
97B PHE 2.5 27.6 - - - +
98B TYR 4.7 0.7 - - - -
99B ARG* 1.3 77.5 - - - +
101B GLY* 1.3 58.8 + - - +
102B LYS* 2.9 21.6 + - - +
104B HIS* 4.5 7.3 + - - -
86C ARG* 4.7 15.5 - - - +
116C ASP* 3.7 30.3 - - + +
117C GLU* 5.3 4.5 - - - +
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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