Contacts of the helix formed by residues 92 - 110 (chain B) in PDB entry 4DJH
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 THR 92 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LYS 4.2 15.7 - - - +
90B MET 3.2 3.6 + - - -
91B LYS* 1.3 81.5 - - - +
93B ALA* 1.3 68.6 + - - +
95B ASN* 2.8 37.7 + - - +
96B ILE* 2.8 13.2 + - - +
172B PRO* 3.9 10.5 - - - +
1305B PEG 3.0 35.5 + - - -
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Residues in contact with ALA 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B THR* 1.3 73.0 - - - +
94B THR* 1.3 64.1 + - - +
96B ILE* 3.2 9.9 + - - +
97B TYR* 3.2 20.9 + - - -
155B ASP* 3.4 23.6 - - - +
170B ARG* 3.6 27.6 - - + +
171B THR* 4.2 10.3 - - - +
172B PRO* 4.2 9.5 - - - +
175B ALA* 3.8 12.5 - - + +
1302B OLC 4.3 4.9 - - - +
1305B PEG 4.7 0.4 + - - -
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Residues in contact with THR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B THR* 3.2 0.4 + - - -
93B ALA* 1.3 78.0 - - - +
95B ASN* 1.3 61.0 + - - +
97B TYR* 3.0 15.9 + - - +
98B ILE* 2.9 33.0 + - + +
152B MET* 3.8 24.0 - - + -
155B ASP* 3.8 4.6 + - - -
156B ARG* 3.2 11.7 + - - -
170B ARG* 3.2 14.8 + - - +
272B ILE* 4.3 10.1 - - + -
275B LEU* 5.1 4.0 - - + -
276B VAL* 4.2 14.4 - - + -
1305B PEG 3.0 21.7 + - - -
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Residues in contact with ASN 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ILE* 3.1 17.7 - - + +
89B LYS 4.8 0.6 + - - -
90B MET* 2.9 52.5 + - - +
92B THR* 2.8 25.8 + - - +
94B THR* 1.3 73.5 - - - +
96B ILE* 1.3 59.5 + - - +
98B ILE* 3.5 9.8 - - - +
99B PHE* 2.7 26.0 + - - +
272B ILE* 6.1 0.9 - - - +
334B ASP* 4.9 3.4 + - - +
336B ASN* 6.0 0.2 - - - +
337B PHE* 3.3 28.6 - - - -
1305B PEG 5.2 0.4 - - - -
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Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ILE* 4.4 16.6 - - + -
91B LYS* 4.5 11.0 - - + -
92B THR 2.8 20.3 + - - +
93B ALA 3.6 5.6 - - - +
95B ASN* 1.3 79.4 - - - +
97B TYR* 1.3 61.5 + - - +
99B PHE* 3.4 6.9 + - + +
100B ASN 3.2 10.4 + - - -
172B PRO* 3.8 27.4 - - + +
175B ALA* 3.1 37.0 - - + -
176B LYS* 3.6 16.2 - - + +
179B ASN* 2.8 32.4 + - - +
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Residues in contact with TYR 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ALA 3.2 24.0 + - - -
94B THR* 3.0 10.4 + - - +
96B ILE* 1.3 73.9 - - - +
98B ILE* 1.3 66.3 + - - +
100B ASN* 2.8 6.1 + - - +
101B LEU* 2.7 20.6 + - - +
148B THR* 3.4 22.6 - - + +
151B MET* 3.7 30.2 + - + +
152B MET* 4.0 22.7 - - + -
155B ASP* 3.6 18.6 - - + -
175B ALA* 4.1 13.8 - - + -
178B ILE* 3.6 29.1 - - + +
179B ASN* 3.4 20.2 - - - -
182B ILE* 5.4 0.7 - - + -
1302B OLC 2.8 30.5 + - - -
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 3.7 24.9 - - + -
84B ILE* 3.9 4.7 - - + -
94B THR* 2.9 17.6 + - + +
95B ASN* 3.2 28.9 + - - +
97B TYR* 1.3 74.0 - - - +
99B PHE* 1.3 57.9 + - - +
101B LEU* 3.1 8.0 + - - +
102B ALA* 2.8 29.3 + - - +
152B MET* 3.2 30.5 - - + +
275B LEU* 4.3 12.3 - - + -
330B TYR* 3.8 26.0 + - + +
337B PHE* 3.6 17.9 - - + -
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Residues in contact with PHE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 4.9 0.4 - - - -
81B MET* 3.6 45.4 - - + +
84B ILE* 3.8 22.7 - - + -
85B ILE* 3.7 28.9 - - + -
95B ASN 2.7 16.7 + - - +
96B ILE* 3.5 13.7 - - + +
97B TYR 3.1 0.2 - - - -
98B ILE* 1.3 72.1 - - - +
100B ASN* 1.3 67.3 + - + +
102B ALA* 3.2 5.7 + - - +
103B LEU* 2.8 47.8 + - + +
179B ASN* 5.4 1.8 - - - -
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Residues in contact with ASN 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ILE 3.2 1.4 + - - -
97B TYR 2.8 6.9 + - - +
99B PHE* 1.3 86.6 - - - +
101B LEU* 1.3 62.9 + - - +
103B LEU* 3.3 10.3 + - - +
104B ALA* 3.2 19.9 + - - +
144B THR* 3.7 8.0 - - - +
148B THR* 2.9 23.9 + - - +
179B ASN* 3.2 40.7 + - - +
182B ILE* 4.5 5.1 - - - +
183B TRP* 2.8 38.8 + - - +
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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
----------------------------------------------------------
97B TYR 2.7 15.6 + - - +
98B ILE* 3.4 9.4 - - - +
100B ASN* 1.3 73.1 - - - +
102B ALA* 1.3 57.9 + - - +
104B ALA* 2.9 9.9 + - - +
105B ASP* 2.8 38.6 + - - +
145B SER* 3.7 38.4 - - - +
148B THR* 4.2 10.5 - - + +
149B LEU* 3.6 32.1 - - + -
152B MET* 4.9 5.8 - - - -
279B VAL* 4.1 7.2 - - + -
283B PHE* 5.2 2.0 - - + -
326B ASN* 3.8 12.3 - - - +
330B TYR* 3.2 21.8 - - + +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN* 3.1 42.9 - - + +
80B VAL* 4.0 19.3 - - + -
81B MET* 4.3 4.0 - - + -
98B ILE 2.8 19.1 + - - +
99B PHE 3.8 2.7 - - - +
101B LEU* 1.3 73.9 - - - +
103B LEU* 1.3 53.9 + - - +
105B ASP* 4.1 1.8 - - - -
106B ALA* 2.7 35.9 + - - +
330B TYR* 4.6 4.9 + - + -
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B MET* 3.6 28.2 - - + -
99B PHE* 2.8 34.1 + - + +
100B ASN* 3.4 8.7 - - - +
102B ALA* 1.3 76.9 - - - +
104B ALA* 1.3 59.5 + - - +
106B ALA* 3.7 1.8 + - + +
107B LEU* 3.2 40.2 + - + +
183B TRP* 4.0 30.1 - - + +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ASN 3.2 3.0 + - - +
101B LEU 2.9 9.7 + - - +
103B LEU* 1.3 79.5 - - - +
105B ASP* 1.3 60.7 + - - +
107B LEU* 3.4 6.8 + - - +
108B VAL 3.2 13.0 + - - -
141B ASN* 2.7 35.3 + - - +
144B THR* 3.6 29.8 - - + -
145B SER* 4.3 13.0 - - - -
183B TRP* 4.8 5.4 - - + -
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Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN* 3.5 29.5 - - - +
101B LEU* 2.8 28.3 + - - +
102B ALA* 4.2 0.2 - - - -
104B ALA* 1.3 74.7 - - - +
106B ALA* 1.3 59.3 + - - +
108B VAL* 3.2 13.4 - - - +
109B THR* 2.7 28.4 + - - -
141B ASN* 4.2 5.7 + - - -
145B SER* 4.8 3.8 - - - -
283B PHE* 5.8 0.2 - - - -
322B ASN* 4.5 4.5 + - - -
323B SER* 3.5 22.1 + - - +
326B ASN* 2.5 35.3 + - - +
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLY 4.5 3.4 - - - -
74B LEU* 3.8 14.2 - - + +
77B ASN* 3.9 16.4 - - + -
78B SER* 4.9 1.6 - - - +
81B MET* 4.1 17.9 - - + -
102B ALA 2.7 21.3 + - - +
103B LEU* 3.9 5.4 - - + +
105B ASP* 1.3 72.4 - - - +
107B LEU* 1.3 66.6 + - + +
109B THR* 3.1 15.5 + - - -
110B THR* 3.3 18.0 + - - +
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Residues in contact with LEU 107 (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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103B LEU* 3.2 30.9 + - + +
104B ALA* 3.4 5.8 + - - +
105B ASP 3.4 0.2 - - - -
106B ALA* 1.3 80.7 - - + +
108B VAL* 1.3 61.5 + - - +
110B THR* 2.6 33.0 + - + +
111B THR* 3.7 0.5 - - - +
137B ILE* 3.7 32.3 - - + +
140B TYR* 5.8 4.0 - - + -
141B ASN* 5.8 1.3 - - + -
183B TRP* 4.0 26.7 - - + -
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ALA 3.2 1.6 + - - -
105B ASP 3.2 14.1 - - - +
107B LEU* 1.3 79.0 - - - +
109B THR* 1.3 65.6 + - - +
111B THR* 2.6 27.5 + - + +
137B ILE* 4.0 11.6 - - - +
138B ASP* 5.2 0.4 - - - +
141B ASN* 3.2 39.7 - - + +
320B TYR* 3.3 8.9 - - + -
323B SER* 3.3 20.0 - - - +
1300B JDC 3.7 43.3 - - + -
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Residues in contact with THR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 3.3 48.2 - - + +
73B GLY* 3.8 10.8 - - - -
74B LEU* 3.5 17.3 - - + +
105B ASP 2.7 18.7 + - - -
106B ALA 3.1 9.3 + - - -
107B LEU 3.1 0.4 - - - -
108B VAL* 1.3 77.0 - - - +
110B THR* 1.3 60.5 + - - +
111B THR 3.0 6.6 + - - -
112B MET* 3.0 29.1 + - - +
320B TYR* 4.6 2.1 + - - -
323B SER* 3.9 12.0 - - - -
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Residues in contact with THR 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 4.6 5.4 - - - -
74B LEU* 3.9 20.4 - - + -
106B ALA 3.3 16.1 + - - +
107B LEU* 2.6 26.3 + - + +
109B THR* 1.3 75.3 - - - +
111B THR* 1.3 61.1 + - - +
112B MET 3.4 0.2 - - - -
113B PRO* 3.3 11.3 - - - +
114B PHE* 3.2 25.0 - - - -
137B ILE* 4.5 8.1 - - - +
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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