Contacts of the helix formed by residues 69 - 90 (chain B) in PDB entry 2AEB
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 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LYS* 3.1 48.0 + - + +
19B GLN 5.2 3.8 + - - -
61B ASP* 3.1 27.2 + - - +
63B PRO* 5.1 1.0 - - - +
68B LYS* 1.3 81.8 - - - +
70B PRO* 1.3 72.0 - - - +
72B SER* 3.2 3.7 + - - -
73B VAL* 3.0 20.8 + - - +
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Residues in contact with PRO 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ASP* 3.5 8.3 - - - +
62B SER 3.4 24.2 - - - +
63B PRO* 4.2 0.9 - - + -
64B PHE* 4.1 13.5 - - + +
67B VAL* 3.6 9.0 - - + +
68B LYS* 3.2 5.3 - - - -
69B ASN* 1.3 89.3 - - - +
71B ARG* 1.3 61.7 + - - +
74B GLY* 2.9 26.0 + - - -
140B LEU* 3.9 15.0 - - + -
159B VAL* 3.7 20.6 - - + -
160B PRO* 3.4 19.1 - - + +
162B PHE* 3.4 9.6 - - + -
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Residues in contact with ARG 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 3.6 16.8 - - + +
60B ASN 4.2 12.7 + - - -
61B ASP* 2.9 28.3 + - - +
62B SER* 2.6 54.2 + - - +
63B PRO 5.3 1.4 + - - -
70B PRO* 1.3 74.5 - - - +
72B SER* 1.3 56.5 + - - +
75B LYS* 2.9 33.3 + - - +
160B PRO* 3.8 43.7 - - + +
161B GLY* 4.1 8.0 - - - +
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Residues in contact with SER 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.7 6.8 - - - -
17B LYS* 3.6 37.8 + - - +
58B ILE* 3.6 25.5 + - - +
61B ASP* 2.7 24.4 + - - +
69B ASN* 3.2 6.0 + - - -
71B ARG* 1.3 77.9 - - - +
73B VAL* 1.3 57.5 + - - +
75B LYS* 3.9 1.0 - - - +
76B ALA* 3.0 30.8 + - - +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.6 10.7 - - + -
17B LYS 3.5 33.2 - - - +
18B GLY* 3.8 5.2 - - - +
69B ASN* 3.0 20.0 + - + +
70B PRO 3.9 0.2 - - - +
72B SER* 1.3 77.6 - - - +
74B GLY* 1.3 61.8 + - - +
76B ALA* 3.4 1.4 + - - +
77B SER* 3.1 23.2 + - - -
102B SER* 3.5 31.0 - - - +
103B LEU* 6.0 0.2 - - - +
105B ILE* 5.0 2.9 - - + -
140B LEU* 3.6 24.9 - - + -
162B PHE* 3.8 16.2 - - + -
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Residues in contact with GLY 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PRO 2.9 15.8 + - - -
71B ARG 3.9 0.2 - - - -
73B VAL* 1.3 77.6 - - - +
75B LYS* 1.4 57.3 + - - +
77B SER* 3.4 0.8 + - - -
78B GLU* 3.0 23.8 + - - +
161B GLY 3.3 21.8 - - - -
162B PHE* 3.6 19.2 - - - -
164B TRP* 3.3 11.6 + - - -
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Residues in contact with LYS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ALA* 6.2 1.0 - - - +
58B ILE* 4.4 14.1 - - + -
71B ARG 2.9 19.2 + - - +
72B SER 3.9 2.9 - - - +
74B GLY* 1.4 74.5 - - - +
76B ALA* 1.3 66.7 + - - +
78B GLU* 3.2 22.9 + - + +
79B GLN* 2.9 53.5 + - - +
161B GLY* 4.1 2.5 + - - -
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.8 24.5 - - + -
55B PHE* 3.7 36.2 - - + -
72B SER 3.0 17.9 + - - +
73B VAL 4.0 3.6 - - - +
75B LYS* 1.3 77.0 - - - +
77B SER* 1.4 58.5 + - - +
79B GLN* 3.4 2.2 + - - +
80B LEU* 2.9 28.6 + - - +
103B LEU* 4.3 7.2 - - + -
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Residues in contact with SER 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL 3.1 18.2 + - - -
74B GLY* 4.9 0.9 - - - -
76B ALA* 1.4 79.9 - - - +
78B GLU* 1.3 51.6 + - - +
80B LEU* 3.2 2.6 + - - -
81B ALA* 2.7 32.4 + - - +
102B SER 3.2 19.8 + - - -
103B LEU* 3.5 10.2 - - - +
105B ILE* 3.7 7.9 - - - +
106B GLY* 3.0 35.2 + - - -
164B TRP* 3.6 15.0 - - - -
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLY 3.0 17.7 + - - +
75B LYS* 3.4 25.1 - - + +
77B SER* 1.3 75.6 - - - +
79B GLN* 1.3 61.5 + - - +
81B ALA* 3.4 3.1 + - - +
82B GLY* 3.2 17.2 + - - -
113B ARG* 5.0 2.9 + - - +
161B GLY 5.0 1.0 - - - +
164B TRP* 3.2 55.6 - - + +
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Residues in contact with GLN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 4.1 12.6 - - + +
54B PRO* 2.8 48.6 + - - +
55B PHE* 3.1 28.4 - - + -
56B ALA 5.0 0.5 + - - -
75B LYS* 2.9 41.1 + - - +
76B ALA* 3.6 4.4 - - - +
78B GLU* 1.3 70.4 - - - +
80B LEU* 1.3 65.4 + - - +
82B GLY* 3.3 3.4 + - - -
83B LYS* 3.2 21.3 + - - +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 3.9 17.0 - - + -
13B ALA* 4.7 3.1 - - + -
53B LEU* 3.7 24.8 - - + +
76B ALA 2.9 18.7 + - - +
77B SER* 3.6 5.6 - - - +
79B GLN* 1.3 75.8 - - - +
81B ALA* 1.3 56.6 + - - +
83B LYS* 3.1 1.8 + - + +
84B VAL* 2.9 48.9 + - + +
96B VAL* 4.0 21.5 - - + -
103B LEU* 3.2 49.4 - - + +
106B GLY* 4.4 0.2 - - - -
107B SER* 3.7 11.9 - - - +
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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
----------------------------------------------------------
77B SER 2.7 20.0 + - - +
78B GLU 3.6 5.4 - - - +
80B LEU* 1.3 73.8 - - - +
82B GLY* 1.4 62.4 + - - +
85B ALA* 3.0 22.3 + - - +
106B GLY* 3.2 21.5 + - - +
110B GLY* 3.3 16.7 - - - +
113B ARG* 3.7 25.2 + - - +
164B TRP* 3.8 11.4 - - + -
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Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLU 3.2 11.5 + - - -
79B GLN* 3.3 4.1 + - - -
80B LEU 3.2 0.4 - - - -
81B ALA* 1.4 81.5 - - - +
83B LYS* 1.3 60.6 + - - +
85B ALA* 3.6 3.6 + - - +
86B GLU* 3.1 21.5 + - - +
113B ARG* 3.9 12.0 - - - +
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Residues in contact with LYS 83 (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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11B ILE* 4.0 25.4 - - + -
50B TYR* 4.3 30.5 - - + +
53B LEU* 3.7 28.3 - - + -
79B GLN 3.2 11.9 + - - +
80B LEU* 3.1 7.7 + - - +
82B GLY* 1.3 74.8 - - - +
84B VAL* 1.3 66.6 + - - +
86B GLU* 3.0 29.0 + - - +
87B VAL* 2.9 27.9 + - + +
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Residues in contact with VAL 84 (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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11B ILE* 3.7 16.4 - - + +
80B LEU* 2.9 30.9 + - + +
81B ALA 4.0 3.1 - - - +
83B LYS* 1.3 76.9 - - - +
85B ALA* 1.3 55.7 + - - +
87B VAL* 2.8 12.5 - - - +
88B LYS* 2.8 28.5 + - + +
94B SER* 3.8 20.0 - - - +
96B VAL* 4.0 13.2 - - + -
107B SER* 3.6 20.6 - - - +
110B GLY* 4.3 1.6 - - - -
111B HIS* 3.5 29.4 - - + +
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Residues in contact with ALA 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 3.0 19.0 + - - +
82B GLY* 3.8 6.1 - - - +
84B VAL* 1.3 75.5 - - - +
86B GLU* 1.3 56.1 + - - +
88B LYS* 3.3 1.0 + - - -
89B LYS* 2.8 42.9 + - - +
110B GLY* 3.6 19.9 + - - +
113B ARG* 4.4 15.0 - - + +
114B VAL* 3.7 14.0 - - + +
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Residues in contact with GLU 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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50B TYR* 3.8 16.1 - - + -
82B GLY 3.1 13.1 + - - +
83B LYS* 3.0 33.1 + - - +
85B ALA* 1.3 72.2 - - - +
87B VAL* 1.3 67.6 + - + +
89B LYS* 3.1 9.4 + - - +
90B ASN* 2.8 49.5 + - - +
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLY* 4.8 6.1 - - - +
11B ILE* 3.9 13.5 - - + -
50B TYR* 3.7 50.5 - - + -
83B LYS* 2.9 13.4 + - + +
84B VAL* 2.8 26.5 - - - +
86B GLU* 1.3 72.4 - - + +
88B LYS* 1.3 68.0 + - - +
90B ASN* 3.1 10.7 + - - +
91B GLY 3.4 0.2 + - - -
92B ARG* 3.3 19.9 + - + +
94B SER* 3.4 35.7 - - - +
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Residues in contact with LYS 88 (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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84B VAL* 2.8 28.2 + - + +
85B ALA* 3.8 4.3 - - - +
87B VAL* 1.3 75.7 - - - +
89B LYS* 1.3 55.0 + - - +
91B GLY* 2.7 25.7 + - - -
92B ARG 2.7 29.7 + - - +
93B ILE* 3.7 2.2 - - - +
94B SER* 3.9 13.7 - - - +
111B HIS* 3.7 24.5 - - + -
114B VAL* 3.9 24.8 - - + +
115B HIS* 3.8 14.5 + - + -
271B SER* 2.8 48.6 + - - +
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Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ALA* 2.8 38.8 + - - +
86B GLU* 3.1 11.8 + - - +
88B LYS* 1.3 75.2 - - - +
90B ASN* 1.3 64.6 + - - +
91B GLY* 3.1 5.2 + - - -
113B ARG* 6.2 2.0 - - - +
114B VAL* 4.3 19.2 - - + +
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Residues in contact with ASN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TYR* 3.0 34.6 + - - +
86B GLU* 2.8 31.2 + - - +
87B VAL 3.6 3.6 - - - +
88B LYS 3.1 0.6 - - - -
89B LYS* 1.3 81.7 - - - +
91B GLY* 1.3 58.9 + - - +
92B ARG* 2.9 36.0 + - - +
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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