Contacts of the helix formed by residues 80 - 98 (chain B) in PDB entry 2JI8
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 SER 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE 3.9 8.9 + - - -
35B PRO* 4.1 6.1 - - - +
79B VAL* 1.3 74.0 - - - +
81B ALA* 1.3 68.8 + - - +
82B PRO 2.9 4.5 - - - -
83B GLY* 3.0 13.3 + - - -
84B PHE* 4.0 0.7 - - - -
106B GLY 3.3 12.5 + - - -
107B SER* 4.0 4.6 - - - -
108B SER* 4.0 10.6 + - - -
120B TYR* 4.3 5.2 - - - -
121B GLU* 2.9 39.9 + - - +
125B GLN* 3.2 17.7 - - - -
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A TRP* 3.7 20.2 - - + -
80B SER* 1.3 69.5 - - - +
82B PRO* 1.4 70.2 - - + +
84B PHE* 3.3 4.0 + - - +
85B LEU* 2.9 32.1 + - - +
121B GLU* 3.5 27.8 + - + +
123B MET* 4.1 23.1 - - + -
125B GLN* 3.1 11.9 + - - -
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Residues in contact with PRO 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 5.5 2.2 - - - +
425A TRP* 3.8 23.8 - - + +
427A VAL* 3.8 25.4 - - + -
1566A TPP 3.7 21.8 - - + +
80B SER 3.1 6.3 - - - +
81B ALA* 1.4 93.4 - - + +
83B GLY* 1.3 60.2 + - - +
85B LEU* 3.4 7.0 + - + +
86B ASN* 3.2 29.1 + - - +
121B GLU* 3.4 28.9 - - + +
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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
----------------------------------------------------------
1566A TPP 3.6 3.8 - - - +
56B GLU* 3.7 24.2 - - - +
78B THR* 3.6 6.6 + - - -
79B VAL* 3.6 19.7 - - - +
80B SER 3.0 8.3 + - - -
82B PRO* 1.3 79.1 - - - +
84B PHE* 1.3 62.6 + - - +
86B ASN* 3.2 6.6 + - - +
87B GLY 3.2 16.8 + - - -
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Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B THR* 3.4 9.9 - - - -
79B VAL 2.9 18.3 + - - +
80B SER 4.1 0.2 - - - -
81B ALA 3.3 5.8 + - - +
83B GLY* 1.3 74.7 - - - +
85B LEU* 1.3 60.1 + - + +
87B GLY* 3.1 2.8 + - - -
88B VAL* 2.8 41.9 + - + +
103B LEU* 3.9 11.2 - - + +
105B SER* 3.5 5.8 - - - +
123B MET* 3.7 13.0 - - - -
125B GLN* 3.3 49.4 - - + +
128B VAL* 3.8 23.6 - - + -
129B ALA* 3.9 12.6 - - + -
165B TYR* 3.4 45.1 - + - -
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 6.0 1.8 - - + -
89A THR* 3.9 30.6 - - + +
92A ALA* 3.7 30.1 - - + -
132A HIS* 3.9 23.6 - - + +
425A TRP* 4.1 8.7 - - + -
81B ALA 2.9 19.5 + - - +
82B PRO* 3.6 7.4 - - + +
83B GLY 3.3 0.2 - - - -
84B PHE* 1.3 73.9 - - + +
86B ASN* 1.3 64.3 + - - +
88B VAL* 3.3 22.5 + - + +
89B THR* 3.3 19.0 + - - +
123B MET* 3.9 18.6 - - + -
128B VAL* 4.2 13.9 - - + -
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Residues in contact with ASN 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN* 2.8 27.8 + - - +
61A TYR* 4.9 3.3 + - - -
89A THR* 4.6 3.0 - - - -
428A MET 5.0 1.0 + - - -
457A PHE* 4.5 1.8 - - - -
1566A TPP 3.6 12.5 - - - +
55B HIS* 3.2 32.5 + - + +
56B GLU* 2.8 28.5 + - + +
57B GLN* 3.6 10.9 - - - +
82B PRO 3.2 14.1 + - - +
83B GLY 3.2 7.4 + - - +
85B LEU* 1.3 79.0 - - - +
87B GLY* 1.3 57.6 + - - +
89B THR* 2.4 32.8 + - - -
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Residues in contact with GLY 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLU* 4.0 18.7 - - - +
76B CYS* 5.0 2.5 - - - -
78B THR* 4.5 1.3 - - - -
83B GLY 3.2 6.8 + - - -
84B PHE 3.1 6.3 + - - -
86B ASN* 1.3 77.8 - - - +
88B VAL* 1.3 58.6 + - - +
90B SER* 3.0 21.8 + - - -
91B LEU* 3.1 11.1 + - - +
101B MET* 4.4 3.5 - - - +
103B LEU* 3.9 20.4 - - - +
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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
----------------------------------------------------------
85A LEU* 6.2 1.6 - - + -
84B PHE* 2.8 42.3 + - + +
85B LEU* 3.3 29.3 + - + +
87B GLY* 1.3 70.2 - - - +
89B THR* 1.3 69.6 + - + +
91B LEU* 4.0 18.2 - - + -
92B ALA* 2.9 25.3 + - - +
103B LEU* 3.7 6.2 - - + +
128B VAL* 5.2 1.3 - - + -
129B ALA* 4.2 5.2 - - - -
132B HIS* 3.8 38.1 - - + +
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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
----------------------------------------------------------
85A LEU* 3.9 38.8 - - + +
86A ASN* 4.4 2.9 - - - +
89A THR* 3.7 23.8 - - + -
57B GLN* 3.1 28.0 + - - +
61B TYR* 4.7 4.7 + - - -
85B LEU 3.3 16.5 + - - +
86B ASN* 2.4 26.9 + - - +
88B VAL* 1.3 79.1 - - + +
90B SER* 1.3 60.1 + - - +
92B ALA* 3.6 4.3 - - - +
93B HIS* 3.4 18.9 + - - +
425B TRP* 4.7 0.7 - - - -
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Residues in contact with SER 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLN* 2.6 40.0 + - - +
60B GLY* 3.5 29.2 - - - -
61B TYR* 3.5 14.7 - - - -
64B SER* 4.8 0.3 - - - -
87B GLY 3.0 9.7 + - - -
89B THR* 1.3 76.3 + - - +
91B LEU* 1.3 59.9 + - - +
92B ALA 3.2 0.4 - - - -
93B HIS* 3.2 7.4 + - - +
94B ALA* 2.9 27.4 + - - +
101B MET* 4.3 3.1 - - - +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLY 3.1 8.0 + - - +
88B VAL* 3.3 27.8 + - + +
90B SER* 1.3 75.1 - - - +
92B ALA* 1.3 63.0 + - - +
94B ALA* 3.2 2.8 + - - +
95B THR* 3.0 28.1 + - - -
101B MET* 3.9 28.3 - - + +
103B LEU* 4.0 15.3 - - + -
132B HIS 3.5 5.4 - - - +
133B CYS* 3.7 22.7 - - + -
163B GLY* 3.6 21.3 - - - -
164B VAL 3.5 24.7 - - - +
165B TYR* 3.9 16.2 - - + -
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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
----------------------------------------------------------
85A LEU* 3.9 15.7 - - + -
88B VAL 2.9 17.0 + - - +
89B THR 3.6 6.7 - - - +
91B LEU* 1.3 75.8 - - - +
93B HIS* 1.3 57.3 + - - +
95B THR* 3.4 3.6 + - - -
96B THR* 2.9 31.7 + - - -
132B HIS* 3.4 36.8 + - + +
425B TRP* 3.8 11.1 - - + -
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Residues in contact with HIS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TYR* 3.5 29.2 - + + +
64B SER* 3.8 14.3 + - - -
89B THR 3.4 10.3 + - - +
90B SER 3.2 8.2 + - - +
92B ALA* 1.3 76.2 - - - +
94B ALA* 1.3 68.0 + - - +
96B THR* 3.4 2.0 + - - -
97B ASN* 2.9 57.4 + - - -
99B PHE* 4.4 4.2 - - - -
421B ASP 5.4 0.2 - - - -
422B SER 4.1 11.4 - - - -
425B TRP* 3.7 18.9 - - + -
427B VAL* 3.6 16.8 - - + +
430B ILE* 3.9 13.5 - - + +
434B TYR* 2.9 29.5 + - - -
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Residues in contact with ALA 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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64B SER* 3.9 9.6 - - - -
90B SER 2.9 13.5 + - - +
91B LEU* 3.2 9.4 + - - +
93B HIS* 1.3 81.2 - - - +
95B THR* 1.3 52.2 + - - +
97B ASN 3.0 2.3 + - - -
98B CYS 2.8 31.5 + - - -
99B PHE* 3.0 32.5 + - + +
101B MET* 3.9 24.0 - - + -
163B GLY 4.7 3.1 - - - +
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Residues in contact with THR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU 3.0 8.9 + - - -
92B ALA 3.8 3.4 - - - -
93B HIS 3.3 0.2 - - - -
94B ALA* 1.3 74.8 - - - +
96B THR* 1.3 63.3 + - - +
97B ASN 3.4 0.3 + - - -
98B CYS* 3.4 14.4 + - - -
131B PRO 5.7 1.3 - - - +
132B HIS 3.1 22.1 + - - +
133B CYS* 3.5 21.1 - - - +
134B LYS* 4.3 10.8 - - + +
160B ARG* 5.3 4.2 - - - +
161B PRO 4.7 1.6 - - - +
162B GLY* 4.1 2.9 - - - -
163B GLY* 3.0 27.8 + - - +
282B ARG* 5.5 0.7 + - - -
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Residues in contact with THR 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 ALA 2.9 18.2 + - - -
93B HIS 3.6 6.3 - - - -
94B ALA 3.3 0.2 - - - -
95B THR* 1.3 79.0 - - - +
97B ASN* 1.3 57.3 + - - +
98B CYS* 4.4 0.2 - - - -
282B ARG* 2.8 31.1 + - - +
424B THR* 3.8 25.2 + - + -
425B TRP* 3.5 41.3 - - + +
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Residues in contact with ASN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B HIS* 2.9 51.3 + - - +
94B ALA 3.0 4.3 + - - +
96B THR* 1.3 79.1 - - - +
98B CYS* 1.3 72.9 + - - +
99B PHE* 3.7 26.6 - - + -
222B LYS* 3.1 36.7 + - - +
282B ARG* 4.5 0.4 - - - -
423B GLY* 3.5 5.9 - - - -
424B THR* 2.9 34.4 + - - +
425B TRP* 4.6 4.0 - - - +
1565B ADP 3.9 2.3 + - - +
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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
----------------------------------------------------------
94B ALA 2.8 7.5 + - - -
95B THR 3.4 6.3 + - - -
96B THR 4.4 1.1 - - - -
97B ASN* 1.3 82.3 - - - +
99B PHE* 1.3 60.7 + - - +
100B PRO* 3.9 2.1 - - - +
160B ARG* 3.7 31.6 - - + -
161B PRO* 3.1 40.3 - - + +
226B TYR* 4.9 6.2 - - - -
282B ARG* 3.9 16.4 - - - -
1565B ADP 3.8 33.9 - - + -
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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
------------------------------------------------------------
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