Contacts of the helix formed by residues 88 - 109 (chain B) in PDB entry 4IXU
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 88 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B GLN* 3.1 61.4 - - + +
37B GLN 4.9 2.1 - - - +
79B ASP* 3.1 28.8 + - - +
81B LEU* 4.7 1.2 - - - +
87B VAL* 1.3 83.0 - - - +
89B PRO* 1.4 70.9 - - - +
91B SER* 4.7 0.4 + - - -
92B VAL* 3.0 21.5 + - - +
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Residues in contact with PRO 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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79B ASP* 3.3 11.7 - - - +
80B ASP 3.7 6.7 - - - +
82B TYR* 3.9 20.9 - - + -
86B ILE* 3.5 17.5 - - + +
87B VAL 3.3 4.7 - - - -
88B ASN* 1.4 90.0 - - - +
90B ARG* 1.3 68.9 + - - +
93B GLY* 2.8 25.1 + - - -
159B LEU* 3.7 15.9 - - + -
178B LEU* 4.5 12.3 - - + -
179B PRO* 3.5 17.6 - - + +
181B PHE* 3.1 11.2 - - + -
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Residues in contact with ARG 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 3.7 28.3 - - + +
77B PRO 5.3 0.2 - - - -
78B LYS 4.5 5.9 + - - -
79B ASP* 2.8 35.2 + - - +
80B ASP* 2.9 35.0 + - - +
81B LEU 4.9 4.6 + - - -
82B TYR* 5.7 1.0 - - - +
89B PRO* 1.3 83.1 - - - +
91B SER* 1.3 57.3 + - - +
93B GLY* 3.7 0.3 - - - -
94B LEU* 2.8 32.4 + - - +
179B PRO* 3.6 44.0 - - + +
180B GLY* 4.3 7.7 - - - +
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Residues in contact with SER 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLN* 3.1 34.1 + - - -
74B THR 5.0 4.4 - - - +
75B PRO* 5.4 1.5 - - - +
76B VAL* 4.0 22.6 + - - +
79B ASP* 2.6 35.5 + - - +
88B ASN 3.9 2.0 - - - -
90B ARG* 1.3 71.1 - - - +
92B VAL* 1.3 59.6 + - - +
94B LEU* 3.9 0.7 - - - +
95B ALA* 2.9 32.8 + - - +
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PHE* 4.5 6.1 - - + -
35B GLN* 3.6 37.2 - - + +
36B GLY* 3.8 7.2 - - - +
88B ASN 3.0 19.7 + - - +
91B SER* 1.3 72.8 - - - +
93B GLY* 1.3 67.3 + - - +
95B ALA* 4.1 4.3 - - - +
96B ASN* 2.9 47.7 + - - +
121B SER* 3.7 20.0 - - - +
124B ILE* 4.8 1.1 - - + -
159B LEU* 3.8 21.1 - - + -
181B PHE* 4.2 7.9 - - + -
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Residues in contact with GLY 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 PRO 2.8 18.1 + - - -
90B ARG 3.7 0.7 - - - -
91B SER 3.2 0.2 - - - -
92B VAL* 1.3 79.0 - - - +
94B LEU* 1.3 55.9 + - - +
96B ASN* 3.4 2.0 + - - -
97B GLN 2.9 22.3 + - - -
180B GLY 3.3 22.7 - - - -
181B PHE* 3.6 13.2 - - - -
183B TRP* 3.1 15.2 + - - -
184B ILE* 5.8 0.4 - - - -
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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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74B THR* 3.5 38.8 - - + +
75B PRO 4.4 0.7 - - - +
76B VAL* 3.9 17.5 - - + -
90B ARG 2.8 21.0 + - - +
91B SER 4.1 2.2 - - - +
93B GLY* 1.3 70.6 - - - +
95B ALA* 1.3 65.9 + - - +
97B GLN* 3.1 21.9 + - + +
98B GLU* 2.9 44.5 + - + +
180B GLY* 4.1 3.0 + - - -
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PHE* 3.4 26.2 - - + -
73B PHE* 3.5 40.1 - - + -
74B THR 5.1 1.4 + - - +
91B SER 2.9 19.0 + - - +
92B VAL* 4.6 0.2 - - - -
94B LEU* 1.3 76.1 - - - +
96B ASN* 1.3 59.3 + - - +
98B GLU* 3.3 2.2 + - - -
99B LEU* 2.8 28.6 + - - +
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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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33B PHE* 3.4 10.0 - - - -
92B VAL* 2.9 42.0 + - - +
93B GLY* 3.7 0.9 - - - +
95B ALA* 1.3 75.4 - - - +
97B GLN* 1.3 59.7 + - - +
99B LEU* 4.3 1.9 - - - +
100B ALA* 2.9 31.7 + - - +
121B SER 3.0 19.8 + - - +
122B LEU* 3.2 16.3 - - - +
124B ILE* 3.8 9.5 - - + +
125B GLY* 2.8 31.4 + - - +
181B PHE* 5.5 0.2 - - - -
183B TRP* 3.6 17.0 - - + -
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Residues in contact with GLN 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 GLY 2.9 14.4 + - - +
94B LEU* 3.5 25.8 - - + +
96B ASN* 1.3 75.9 - - - +
98B GLU* 1.3 63.3 + - + +
100B ALA* 3.4 3.3 + - - +
101B GLU* 3.3 21.1 + - - +
132B ARG* 5.0 4.1 + - - +
180B GLY 5.4 0.2 - - - +
183B TRP* 3.3 53.4 - - + +
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Residues in contact with GLU 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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71B LEU* 5.4 0.4 - - + -
72B SER 4.3 2.5 - - - +
73B PHE* 3.4 20.4 - - + +
74B THR* 2.5 50.9 + - - -
94B LEU* 2.9 33.0 + - + +
95B ALA* 3.6 4.1 - - - +
97B GLN* 1.3 75.0 - - + +
99B LEU* 1.3 64.6 + - - +
101B GLU* 3.3 14.9 + - - +
102B VAL* 3.3 18.4 + - - +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 3.9 28.5 - - + -
31B ALA* 4.1 8.1 - - + -
33B PHE* 3.9 10.5 - - + -
71B LEU* 4.0 11.0 - - + -
73B PHE* 4.0 8.9 - - + -
95B ALA 2.8 18.2 + - - +
96B ASN* 3.8 6.1 - - - +
98B GLU* 1.3 76.9 - - - +
100B ALA* 1.3 58.3 + - - +
102B VAL* 3.0 2.8 + - - -
103B VAL* 2.9 38.2 + - + +
115B THR* 4.3 6.7 - - + -
122B LEU* 3.6 40.4 - - + +
126B THR* 3.6 18.8 - - + +
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Residues in contact with ALA 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 ASN 2.9 18.8 + - - +
97B GLN 3.6 6.1 - - - +
99B LEU* 1.3 76.4 - - - +
101B GLU* 1.3 57.7 + - - +
103B VAL* 4.5 0.7 - - - -
104B SER* 2.8 32.1 + - - -
125B GLY 3.3 23.3 + - - +
129B GLY* 3.3 13.6 - - - +
132B ARG* 3.8 20.4 - - - +
183B TRP* 4.0 9.9 - - + -
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Residues in contact with GLU 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 GLN 3.3 9.7 + - - +
98B GLU* 3.5 11.9 - - - +
99B LEU 3.1 0.4 - - - -
100B ALA* 1.3 80.5 - - - +
102B VAL* 1.3 64.5 + - + +
104B SER* 3.5 4.6 + - - -
105B ARG* 3.0 23.8 + - + +
132B ARG* 3.4 19.0 + - - +
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Residues in contact with VAL 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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29B ILE* 3.6 22.9 - - + -
68B PHE* 3.7 30.3 - - + -
71B LEU* 3.9 30.1 - - + -
98B GLU 3.5 13.9 - - - +
99B LEU 3.0 6.6 + - - +
101B GLU* 1.3 74.1 - - + +
103B VAL* 1.3 66.1 + - - +
105B ARG* 3.3 6.1 + - - +
106B ALA* 3.0 22.5 + - - +
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Residues in contact with VAL 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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29B ILE* 3.9 17.7 - - + -
99B LEU* 2.9 30.0 + - + +
100B ALA 3.9 3.6 - - - +
102B VAL* 1.3 74.8 - - - +
104B SER* 1.3 65.0 + - - +
106B ALA* 3.2 2.1 + - - +
107B VAL* 2.9 28.9 + - + +
113B CYS* 4.0 22.2 - - + -
115B THR* 4.1 0.7 - - - +
126B THR* 3.6 43.1 - - + +
129B GLY* 4.0 2.0 - - - -
130B HIS* 3.7 17.5 - - + +
291B ALA* 5.5 2.2 - - + -
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Residues in contact with SER 104 (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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100B ALA 2.8 19.2 + - - -
101B GLU* 3.7 7.6 - - - -
103B VAL* 1.3 77.0 - - - +
105B ARG* 1.3 57.0 + - - +
107B VAL* 3.4 1.5 + - - -
108B SER* 2.9 27.9 + - - -
129B GLY 3.5 17.0 + - - -
132B ARG* 3.7 22.2 - - - -
133B HIS* 3.0 34.2 + - - -
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Residues in contact with ARG 105 (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 LYS* 6.2 1.1 - - - +
68B PHE* 5.9 5.8 - - + -
101B GLU* 3.0 18.9 + - + +
102B VAL* 3.8 5.8 - - - +
103B VAL 3.2 0.4 - - - -
104B SER* 1.3 76.3 - - - +
106B ALA* 1.3 62.8 + - - +
108B SER* 2.7 26.1 + - - -
109B ASP* 2.9 42.4 + - - +
133B HIS* 5.4 0.2 - - - -
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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
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27B ALA* 4.0 27.1 - - + -
29B ILE* 4.9 0.4 - - + -
68B PHE* 4.2 14.7 - - + -
102B VAL 3.0 16.3 + - - +
103B VAL 3.6 4.0 - - - +
105B ARG* 1.3 76.7 - - - +
107B VAL* 1.3 61.4 + - - +
109B ASP* 3.2 7.6 + - - -
110B GLY 3.3 0.2 + - - -
111B TYR* 3.0 33.9 + - + +
113B CYS* 4.0 15.3 - - + -
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Residues in contact with VAL 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 VAL* 2.9 25.9 + - + +
104B SER* 4.0 4.5 - - - +
106B ALA* 1.3 75.9 - - - +
108B SER* 1.3 58.8 + - - +
110B GLY* 2.9 20.6 + - - -
111B TYR 3.7 16.4 - - - +
113B CYS* 4.2 15.7 - - + -
130B HIS* 4.0 22.2 - - + +
133B HIS* 4.2 12.6 - - + -
134B CYS* 3.7 30.1 - - - -
290B SER* 4.5 7.9 - - - +
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Residues in contact with SER 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B SER 2.9 16.2 + - - -
105B ARG* 2.7 36.4 + - - -
107B VAL* 1.3 76.2 - - - +
109B ASP* 1.3 60.3 + - - +
110B GLY* 3.2 1.6 + - - -
133B HIS* 3.4 33.2 + - - -
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Residues in contact with ASP 109 (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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25B SER* 6.0 0.3 - - - -
66B LYS* 4.9 8.8 + - - -
68B PHE* 6.1 0.7 - - - -
105B ARG* 2.9 53.8 + - - +
106B ALA* 3.2 5.6 + - - +
107B VAL 3.2 0.2 - - - -
108B SER* 1.3 77.7 + - - +
110B GLY* 1.3 59.3 + - - +
111B TYR* 3.5 24.7 - - + -
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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