Contacts of the helix formed by residues 80 - 98 (chain B) in PDB entry 4X2Q
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 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ARG 3.6 3.1 + - - +
79B MET* 1.3 82.1 - - - +
81B ALA* 1.3 65.2 + - - +
82B SER* 4.1 8.5 - - - +
83B GLU* 3.2 22.7 + - + +
84B ARG* 3.2 11.3 + - - +
146C VAL 4.5 1.2 - - - +
147C ASP* 3.4 33.1 - - - +
148C GLY* 2.8 31.8 + - - +
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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
----------------------------------------------------------
79B MET 3.8 1.6 + - - -
80B ASP* 1.3 71.8 - - - +
82B SER* 1.3 62.2 + - - +
84B ARG* 3.1 46.9 + - - +
136B ALA* 3.3 16.6 - - - +
137B ASP* 3.8 24.9 - - + -
145C PRO* 3.9 25.1 + - + +
146C VAL 5.8 0.8 + - - -
147C ASP* 4.8 1.2 + - - -
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASP* 4.1 3.8 - - - +
81B ALA* 1.3 78.8 - - - +
83B GLU* 1.3 64.0 + - - +
85B GLY* 3.4 3.6 + - - +
86B ARG* 3.0 31.0 + - - +
136B ALA* 5.1 0.7 - - - -
137B ASP* 3.3 30.5 - - - +
147C ASP* 3.1 32.1 + - - -
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B MET* 3.5 25.3 - - + +
80B ASP* 3.2 25.3 + - + +
81B ALA 3.1 0.6 - - - -
82B SER* 1.3 82.1 + - - +
84B ARG* 1.3 64.7 + - - +
85B GLY 3.2 0.2 - - - -
86B ARG* 3.0 22.0 + - - +
87B LEU* 3.0 31.2 + - - +
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Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TRP* 3.6 45.8 + - + -
79B MET* 4.1 14.1 + - + -
80B ASP 3.2 9.0 + - - +
81B ALA* 3.1 34.8 + - - +
83B GLU* 1.3 77.0 - - - +
85B GLY* 1.3 60.7 + - - +
87B LEU* 3.6 4.0 + - - +
88B LEU* 3.4 26.9 + - - +
136B ALA* 4.4 10.5 + - + +
139B ILE* 5.0 2.0 - - - +
158B PRO* 5.7 3.4 - - - +
183B LEU 3.9 4.0 - - - +
184B CYS 2.5 31.3 + - - -
185B CYS* 3.3 15.6 + - - +
186B GLY* 3.7 23.5 - - - -
145C PRO* 5.9 1.0 - - - +
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Residues in contact with GLY 85 (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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81B ALA 3.3 7.7 + - - -
82B SER 3.4 4.4 + - - -
83B GLU 3.2 0.4 - - - -
84B ARG* 1.3 76.8 - - - +
86B ARG* 1.3 64.3 + - - +
88B LEU* 3.5 2.0 + - - -
89B ASP* 3.0 20.8 + - - +
133B ALA* 3.2 39.0 - - - +
136B ALA* 3.6 9.5 - - - +
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Residues in contact with ARG 86 (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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82B SER* 3.0 21.2 + - - +
83B GLU* 3.0 32.3 + - - +
85B GLY* 1.3 76.8 - - - +
87B LEU* 1.3 63.9 + - + +
89B ASP* 3.1 39.1 + - - +
90B LYS* 3.0 39.1 + - - +
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TRP* 4.0 12.3 - - + -
79B MET* 4.2 14.1 - - + -
83B GLU* 3.0 17.7 + - - +
84B ARG 3.9 3.8 - - - +
85B GLY 3.3 0.2 - - - -
86B ARG* 1.3 74.9 - - + +
88B LEU* 1.3 60.9 + - - +
90B LYS* 3.2 7.6 + - + +
91B LEU* 3.0 22.2 + - - +
211B ALA* 3.3 26.7 - - - +
212B GLY 3.6 21.3 - - - +
213B PHE* 3.6 42.0 - - + +
214B PRO* 3.9 13.5 - - + -
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG 3.4 16.3 + - - +
85B GLY* 3.7 8.1 - - - +
86B ARG 3.3 0.2 - - - -
87B LEU* 1.3 78.3 - - - +
89B ASP* 1.3 60.7 + - - +
91B LEU* 3.1 6.7 + - - +
92B ALA 3.0 19.4 + - - -
129B PHE* 3.9 34.9 - - + +
132B TYR* 3.9 8.7 - - + +
133B ALA* 3.8 29.8 - - + +
136B ALA* 5.2 0.4 - - + -
180B ALA* 4.3 11.4 - - + +
183B LEU* 4.0 33.2 - - + -
184B CYS* 4.1 21.8 - - - +
213B PHE* 4.2 7.6 - - + -
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Residues in contact with ASP 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLY 3.0 17.9 + - - +
86B ARG* 3.1 31.2 + - - +
88B LEU* 1.3 75.8 - - - +
90B LYS* 1.3 57.2 + - - +
92B ALA* 3.5 6.1 + - - +
93B ASP* 3.2 33.8 + - - +
129B PHE 5.0 0.2 - - - -
130B ARG* 3.6 28.8 + - - +
133B ALA* 3.7 14.5 - - + +
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Residues in contact with LYS 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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86B ARG* 3.0 30.6 + - - +
87B LEU* 3.5 13.0 - - + +
88B LEU 3.2 0.2 - - - -
89B ASP* 1.3 73.6 - - - +
91B LEU* 1.3 65.2 + - - +
93B ASP* 3.2 21.9 + - + +
94B LEU* 3.1 32.5 + - + +
210B GLU 5.5 0.2 - - - +
211B ALA* 4.0 28.0 - - + +
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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 LEU 3.0 12.4 + - - +
88B LEU* 3.1 10.7 + - + +
90B LYS* 1.3 74.2 - - - +
92B ALA* 1.3 63.6 + - - +
94B LEU* 3.3 4.6 + - + +
95B VAL* 3.1 28.3 + - + +
129B PHE* 3.6 33.9 - - + -
179B ILE* 5.0 4.5 - - + -
183B LEU* 5.3 0.2 - - + -
204B MET* 4.0 13.7 - - + -
207B LEU* 3.5 42.0 - - + +
208B ILE* 3.8 22.0 - - + +
211B ALA* 4.2 2.2 - - + +
213B PHE* 3.9 21.5 - - + -
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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
----------------------------------------------------------
88B LEU 3.0 8.2 + - - +
89B ASP* 3.6 9.4 - - - +
91B LEU* 1.3 75.5 - - - +
93B ASP* 1.3 50.3 + - - +
95B VAL* 3.3 8.4 + - - +
96B GLU* 2.8 36.0 + - - +
126B ILE* 3.8 16.6 - - + +
129B PHE* 3.8 16.2 - - + +
130B ARG* 3.7 37.0 - - + +
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Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ASP* 3.2 17.5 + - - +
90B LYS* 3.2 29.2 + - + +
92B ALA* 1.3 78.2 - - - +
94B LEU* 1.3 58.6 + - + +
96B GLU* 3.3 6.4 - - - +
97B ARG* 3.0 27.8 + - - +
130B ARG* 2.7 32.6 + - - +
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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
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90B LYS* 3.1 20.5 + - + +
91B LEU* 3.7 6.7 - - - +
92B ALA 3.3 0.2 - - - -
93B ASP* 1.3 78.3 - - + +
95B VAL* 1.3 60.8 + - - +
97B ARG* 3.3 23.3 + - - +
98B ASP* 3.0 33.8 + - - -
207B LEU* 3.4 43.1 - - + +
210B GLU* 3.4 33.0 - - + +
211B ALA* 3.7 24.5 - - + +
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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
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91B LEU 3.1 16.0 + - - +
92B ALA* 3.6 8.3 - - - +
94B LEU* 1.3 72.7 - - - +
96B GLU* 1.3 56.3 + - - +
98B ASP 3.0 2.4 + - - -
99B ARG* 2.7 34.1 + - - -
102B LEU* 3.7 18.8 - - + -
122B LEU* 3.7 17.3 - - + -
125B VAL* 4.0 16.8 - - + -
126B ILE* 3.7 16.2 - - + -
129B PHE* 4.8 2.9 - - + -
172B LEU* 5.3 0.4 - - + -
204B MET* 3.7 34.3 - - + -
207B LEU* 4.0 7.2 - - + -
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Residues in contact with GLU 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 2.8 17.9 + - - +
93B ASP* 3.3 14.4 - - - +
95B VAL* 1.3 73.7 - - - +
97B ARG* 1.3 61.0 + - - +
99B ARG* 3.4 39.8 + - - +
126B ILE* 3.8 30.5 - - + +
130B ARG* 4.3 13.8 + - - +
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Residues in contact with ARG 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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93B ASP 3.0 13.1 + - - +
94B LEU* 3.6 21.6 + - + +
95B VAL 3.2 0.2 - - - -
96B GLU* 1.3 77.1 - - - +
98B ASP* 1.3 92.1 + - - +
99B ARG 3.3 2.2 + - - -
100B ALA* 4.9 3.5 + - - +
203B TYR* 4.8 0.4 + - - -
207B LEU* 3.5 8.9 - - - +
210B GLU* 3.2 38.2 + - - -
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Residues in contact with ASP 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU 3.0 14.3 + - - +
95B VAL 3.0 3.6 + - - -
97B ARG* 1.3 118.4 + - - +
99B ARG* 1.3 64.2 + - - +
100B ALA* 3.1 3.6 - - - -
101B VAL* 3.1 15.8 + - + +
102B LEU* 3.0 28.0 + - + +
203B TYR* 2.5 35.7 + - + +
207B LEU* 3.4 9.9 - - - +
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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
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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