Contacts of the helix formed by residues 87 - 104 (chain B) in PDB entry 4DHI
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 ASN 87 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ASP* 2.9 9.5 + - - +
86B GLY* 1.3 79.3 - - - +
88B CYS* 1.3 64.2 + - - +
89B PHE 3.4 2.2 - - - -
90B TYR* 3.2 7.5 + - - +
91B ARG* 3.0 43.3 + - - +
170B LEU* 3.6 9.5 - - + +
174B ARG* 2.9 20.0 + - - +
209B MET* 3.8 18.4 - - - +
210B TRP* 2.9 61.7 + - - +
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Residues in contact with CYS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ILE* 3.8 12.7 - - - +
83B ARG 3.5 23.3 - - - +
84B GLY* 4.1 8.7 - - - -
85B ASP* 3.0 17.5 + - - +
86B GLY 3.4 1.2 - - - -
87B ASN* 1.3 76.8 - - - +
89B PHE* 1.3 66.0 - - - +
91B ARG* 3.1 3.2 + - - +
92B ALA* 2.9 21.5 + - - +
212B ASP* 5.6 1.6 - - - +
266B GLY 5.2 0.4 - - - +
267B HIS* 4.5 0.9 - - - -
268B TYR* 3.4 46.7 - - + -
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Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLY 5.4 0.2 + - - -
87B ASN 3.3 0.8 + - - -
88B CYS* 1.3 79.5 - - - +
90B TYR* 1.3 64.3 + + + +
92B ALA* 3.3 3.8 + - - +
93B ILE* 3.1 44.1 + - + +
213B ALA* 4.1 22.2 - - + +
218B ILE* 3.5 47.8 - - + -
221B LEU* 3.7 17.9 - - + -
222B ILE* 3.9 11.2 - - + -
231B ILE* 4.1 9.9 - - + -
261B LEU* 3.7 20.9 - - + -
268B TYR* 3.8 47.0 - + + -
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Residues in contact with TYR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLY 4.8 1.1 - - - -
87B ASN 3.2 10.6 + - - +
89B PHE* 1.3 77.1 - - + +
91B ARG* 1.3 58.7 + - - +
93B ILE* 3.4 2.1 + - - +
94B LEU* 2.9 30.7 + - - +
170B LEU* 3.8 21.1 - - + -
173B PHE* 4.3 6.2 - - + -
174B ARG* 3.4 62.8 + - + -
177B THR* 3.7 21.4 - - + +
205B GLU 4.8 0.7 + - - -
206B ILE* 3.9 15.4 - - - +
211B LYS 4.0 3.8 - - - -
213B ALA* 3.8 24.7 - - + +
217B ALA* 3.8 21.7 - - + +
221B LEU* 3.7 30.5 - - + +
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Residues in contact with ARG 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.7 54.4 - - - +
44B VAL* 4.0 12.8 - - + -
82B ILE* 3.7 13.1 - - + +
83B ARG* 5.1 2.8 + - - +
85B ASP* 4.6 6.9 + - - -
87B ASN* 3.0 38.5 + - - +
88B CYS* 3.6 7.4 - - - +
90B TYR* 1.3 74.7 - - - +
92B ALA* 1.3 59.2 + - - +
94B LEU* 3.3 9.9 + - + +
95B VAL* 2.9 37.3 + - + +
160B LEU 5.7 0.2 - - - +
166B ALA* 3.7 30.7 + - - +
167B ASN* 3.1 27.3 + - - +
170B LEU* 3.6 18.8 - - + +
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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
----------------------------------------------------------
82B ILE* 4.0 24.8 - - + +
88B CYS 2.9 15.4 + - - +
89B PHE 3.8 3.8 - - - +
91B ARG* 1.3 76.0 - - - +
93B ILE* 1.3 58.1 + - - +
95B VAL* 3.5 2.3 + - - +
96B GLY* 3.0 24.4 + - - -
259B ILE* 4.7 0.3 - - - +
261B LEU* 3.8 32.0 - - + +
268B TYR* 4.1 12.3 - - + +
270B VAL* 3.8 9.3 - - + +
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 3.1 47.2 + - + +
90B TYR 3.8 3.6 - - - +
92B ALA* 1.3 74.1 - - - +
94B LEU* 1.3 62.4 + - - +
96B GLY* 3.2 1.4 + - - -
97B LEU* 2.9 45.3 + - + +
173B PHE* 5.5 1.3 - - + -
221B LEU* 3.8 24.7 - - + -
222B ILE* 4.4 2.7 - - + -
225B ALA* 5.0 0.9 - - + -
227B THR* 4.6 8.3 - - + -
229B VAL* 3.6 30.1 - - + -
259B ILE* 3.8 14.6 - - + +
261B LEU* 4.0 14.1 - - + -
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR 2.9 20.5 + - - +
91B ARG* 3.4 24.2 - - + +
93B ILE* 1.3 76.1 - - - +
95B VAL* 1.3 63.7 + - + +
97B LEU* 3.7 6.1 - - - +
98B ILE* 2.9 52.0 + - + +
160B LEU* 3.9 17.9 - - + -
166B ALA 5.1 2.2 - - - +
169B ILE* 4.1 6.5 - - + -
170B LEU* 3.8 38.1 - - + +
173B PHE* 3.6 32.3 - - + -
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 3.7 34.3 - - + -
80B ARG* 3.8 30.5 - - - +
82B ILE* 4.2 8.3 - - + -
91B ARG* 2.9 21.7 + - + +
92B ALA 3.8 3.4 - - - +
94B LEU* 1.3 86.3 - - + +
96B GLY* 1.3 62.7 + - - +
98B ILE* 3.3 4.7 + - - +
99B GLU* 2.9 38.5 + - + +
157B TYR* 4.8 5.8 - - + -
160B LEU* 4.5 9.9 - - + -
270B VAL* 4.5 7.4 - - + -
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Residues in contact with GLY 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ALA 3.0 15.1 + - - -
93B ILE 3.7 2.5 - - - -
95B VAL* 1.3 77.0 - - - +
97B LEU* 1.3 61.6 + - - +
99B GLU* 3.4 13.5 + - - +
100B ILE* 3.2 25.8 + - - +
259B ILE* 3.8 25.9 - - - +
270B VAL* 4.8 4.9 - - - +
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 2.9 25.8 + - + +
94B LEU* 3.7 4.5 - - - +
96B GLY* 1.3 73.0 - - - +
98B ILE* 1.3 67.9 + - + +
100B ILE* 3.1 11.3 + - + +
101B MET* 3.0 38.4 + - + +
107B ARG* 4.6 3.1 - - - +
111B PHE* 4.3 15.9 - - + -
173B PHE* 3.8 23.1 - - + -
225B ALA* 3.8 28.9 - - + +
227B THR* 3.5 32.8 - - - +
258B GLU* 4.5 4.9 - - - +
259B ILE* 3.7 8.6 - - + +
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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
----------------------------------------------------------
94B LEU* 2.9 42.3 + - + +
95B VAL* 4.0 4.0 - - - +
97B LEU* 1.3 78.4 - - + +
99B GLU* 1.3 57.8 + - + +
101B MET* 3.1 9.4 + - + +
102B LEU* 2.9 36.8 + - + +
111B PHE* 6.6 0.2 - - + -
139B PHE* 4.6 12.1 - - + -
142B PHE* 3.8 25.1 - - + -
143B LEU* 4.7 11.7 - - + -
146B ILE* 4.4 10.8 - - + -
156B VAL* 3.8 27.4 - - + -
157B TYR* 6.2 1.1 - - + -
160B LEU* 3.9 14.6 - - + -
169B ILE* 4.8 0.7 - - + -
173B PHE* 6.0 0.9 - - + -
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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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80B ARG* 2.8 32.9 + - - -
95B VAL* 2.9 25.3 + - + +
96B GLY* 3.6 12.4 - - - +
97B LEU 3.2 0.2 - - - -
98B ILE* 1.3 79.5 - - + +
100B ILE* 1.3 62.1 + - + +
102B LEU* 3.5 15.6 + - + +
103B LYS* 3.7 21.1 + - + +
157B TYR* 3.0 20.3 + - + +
270B VAL* 4.2 2.6 - - - +
272B TYR* 2.5 37.8 + - + -
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Residues in contact with ILE 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 GLY 3.2 14.1 + - - +
97B LEU* 3.1 15.5 + - + +
99B GLU* 1.3 75.7 - - + +
101B MET* 1.3 65.2 + - + +
103B LYS* 3.1 17.6 + - - +
104B ASP* 3.2 16.9 + - + +
107B ARG* 4.0 33.0 - - + +
258B GLU* 3.6 54.7 - - + +
259B ILE* 4.1 6.7 - - + -
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Residues in contact with MET 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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97B LEU* 3.0 37.1 + - + +
98B ILE* 3.1 11.2 + - + +
100B ILE* 1.3 78.5 - - + +
102B LEU* 1.3 63.4 + - - +
103B LYS 3.2 0.5 + - - -
104B ASP 3.3 20.6 + - - +
105B ARG* 4.2 2.1 + - - +
107B ARG* 3.7 35.0 - - + +
108B LEU* 3.7 49.9 - - + +
111B PHE* 3.6 39.7 - - + -
143B LEU* 5.3 5.4 - - + -
146B ILE* 5.0 4.3 - - + +
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Residues in contact with LEU 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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98B ILE* 2.9 30.8 + - + +
99B GLU* 3.7 10.1 - - - +
100B ILE 3.3 0.6 - - - -
101B MET* 1.3 75.4 - - - +
103B LYS* 1.3 60.9 + - + +
105B ARG* 5.4 6.4 + - - -
146B ILE* 3.8 29.6 - - + -
151B HIS 5.6 1.6 - - - +
152B THR 5.6 0.2 - - - -
153B GLU* 3.9 35.4 - - + +
156B VAL* 4.0 22.0 - - + -
157B TYR* 4.2 20.2 - - + +
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Residues in contact with LYS 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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99B GLU* 3.7 15.9 + - - +
100B ILE* 3.1 10.2 + - - +
101B MET 3.1 0.6 - - - -
102B LEU* 1.3 83.6 - - + +
104B ASP* 1.3 60.0 + - + +
105B ARG 4.2 0.4 - - - -
153B GLU* 6.0 1.6 - - - -
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Residues in contact with ASP 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ILE* 3.2 15.6 + - + +
101B MET* 3.3 10.2 + - - +
102B LEU 3.6 0.2 - - - -
103B LYS* 1.3 81.4 - - + +
105B ARG* 1.3 62.7 + - - +
106B ALA* 3.1 21.7 + - - +
107B ARG* 3.2 24.2 + - + +
108B LEU 3.0 17.0 + - - -
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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