Contacts of the helix formed by residues 58 - 74 (chain B) in PDB entry 2AJA
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 LYS 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B THR* 1.3 101.6 - - + +
59B ASN* 1.3 68.4 + - - +
60B MSE 4.5 5.6 - - + +
61B GLU* 3.6 29.4 + - + +
62B GLN* 3.2 24.5 + - - +
91B LYS* 5.8 0.4 - - - +
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Residues in contact with ASN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LYS* 1.3 70.0 - - - +
60B MSE 1.3 70.5 + - + +
61B GLU 3.0 1.8 - - - -
62B GLN* 2.8 19.1 + - - +
63B VAL* 2.8 21.3 + - + +
91B LYS* 3.3 32.1 + - - +
93B GLU* 3.6 15.0 + - - -
94B VAL* 4.3 9.4 - - + -
97B PHE* 3.4 28.4 - - + -
127B GLU* 3.5 23.4 + - - +
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Residues in contact with MSE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 4.3 34.5 - - + +
31B GLN* 6.0 4.7 - - - +
58B LYS* 3.6 4.6 - - + +
59B ASN* 1.3 78.9 - - + +
61B GLU* 1.3 64.1 + - + +
63B VAL* 3.5 25.7 + - + -
64B ARG* 3.0 37.8 + - - +
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLU* 5.0 1.1 - - - +
56B GLY* 3.3 13.8 - - - -
57B THR* 3.1 28.1 + - - +
58B LYS* 3.6 37.0 + - + +
59B ASN 3.0 0.8 - - - -
60B MSE 1.3 78.5 - - + +
62B GLN* 1.3 64.1 + - - +
63B VAL 3.1 0.3 + - - -
64B ARG* 3.1 12.7 + - - +
65B GLN* 3.1 29.2 + - + +
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Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PRO* 4.6 0.6 - - - +
56B GLY 3.6 23.7 + - - +
57B THR 4.7 2.2 + - - -
58B LYS 3.2 13.2 + - - +
59B ASN 2.8 12.4 + - - +
61B GLU* 1.3 75.5 - - - +
63B VAL* 1.3 55.2 + - - +
65B GLN* 3.4 10.5 + - - +
66B LEU* 3.0 29.6 + - - +
89B GLY 3.5 11.7 + - - -
90B ILE* 2.9 30.4 - - + +
91B LYS* 2.6 50.5 + - - +
94B VAL* 3.4 19.8 - - + +
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 3.9 28.0 - - + -
59B ASN* 2.8 29.2 + - + +
60B MSE 3.6 19.3 - - + +
62B GLN* 1.3 69.5 - - - +
64B ARG* 1.3 70.3 + - - +
65B GLN 3.2 0.2 + - - -
66B LEU* 3.2 3.3 + - - +
67B LEU* 3.1 34.2 + - + +
94B VAL* 4.0 18.6 - - + -
97B PHE* 4.3 21.8 - - + -
98B VAL* 4.7 4.7 - - + -
101B ILE* 4.3 12.3 - - + -
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Residues in contact with ARG 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 4.1 19.3 + - + -
30B PHE* 3.0 58.9 + - + +
31B GLN* 5.2 2.0 - - - +
33B PHE* 2.6 50.9 + - - -
34B ILE* 3.8 1.6 - - - +
38B GLU* 2.7 43.6 + - - +
60B MSE 3.0 27.1 + - - +
61B GLU* 3.6 10.1 - - - +
63B VAL* 1.3 76.6 - - - +
65B GLN* 1.3 58.6 + - - +
67B LEU* 3.7 2.4 - - - +
68B CYS* 2.9 34.4 + - - -
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Residues in contact with GLN 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN* 5.0 8.5 - - - +
38B GLU* 4.8 16.0 + - + +
41B LEU* 4.9 13.1 - - + +
53B PHE* 3.2 35.3 - - + -
54B LEU 3.3 18.4 + - - +
55B PRO* 3.2 5.9 - - - +
56B GLY* 2.8 25.2 + - - +
61B GLU* 3.1 11.1 + - + +
62B GLN* 3.5 17.1 - - - +
63B VAL 3.2 0.2 - - - -
64B ARG* 1.3 77.2 - - - +
66B LEU* 1.3 57.8 + - - +
68B CYS* 3.1 8.5 + - - +
69B LEU* 2.8 35.1 + - + +
90B ILE* 4.2 0.2 - - - +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 5.6 0.6 - - - -
62B GLN 3.0 19.6 + - - +
63B VAL 3.9 0.7 - - - +
65B GLN* 1.3 72.7 - - - +
67B LEU* 1.3 52.5 - - - +
69B LEU* 3.4 8.5 + - + +
70B TYR* 2.6 37.0 + - - +
81B LEU* 4.5 11.2 - - + -
82B TRP* 3.7 24.2 - - + -
85B ALA* 3.9 25.8 - - + -
90B ILE* 4.6 6.5 - - + -
94B VAL* 3.7 7.6 - - + +
95B ILE* 3.6 31.0 - - + +
98B VAL* 3.3 35.9 - - + -
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 5.4 0.2 - - - -
25B LEU* 4.4 12.1 - - + -
29B LEU* 4.0 35.9 - - + -
30B PHE* 4.1 14.6 - - + -
63B VAL* 3.1 20.5 + - + +
64B ARG 3.7 2.5 - - - +
66B LEU* 1.3 72.5 - - - +
68B CYS* 1.3 67.6 + - - +
70B TYR* 4.0 3.4 - - - -
71B TYR* 2.8 43.9 + - + +
98B VAL* 3.6 24.9 - - + -
101B ILE* 4.5 11.2 - - + -
102B THR* 3.7 27.1 - - + -
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Residues in contact with CYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 4.5 5.2 - - - -
30B PHE* 3.6 22.4 - - - -
34B ILE* 3.9 24.2 - - - -
38B GLU* 4.4 16.2 - - + +
41B LEU* 4.8 4.0 - - + -
42B MSE 3.5 28.9 - - + +
64B ARG 2.9 21.7 + - - +
65B GLN* 3.4 11.0 - - - +
67B LEU* 1.3 78.2 - - - +
69B LEU* 1.3 64.3 + - - +
71B TYR* 4.1 0.5 - - - +
72B ALA* 3.3 22.0 + - - +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 3.8 35.2 - - + +
46B TYR* 5.2 1.8 - - + -
49B ALA* 4.0 12.6 - - + -
50B ILE* 4.8 13.2 - - + -
53B PHE* 4.0 36.8 - - + -
65B GLN 2.8 22.2 + - - +
66B LEU* 3.6 10.5 - - + +
68B CYS* 1.3 75.6 - - - +
70B TYR* 1.3 67.0 + - - +
72B ALA* 2.8 3.3 + - - -
73B HIS* 2.8 38.7 + - + +
81B LEU* 4.0 23.6 - - + -
85B ALA* 5.6 0.9 - - + -
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Residues in contact with TYR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 5.2 3.1 - + - -
237A GLU* 3.9 18.4 - - - +
66B LEU 2.6 22.6 + - - +
67B LEU* 3.5 6.7 - - - +
69B LEU* 1.3 71.8 - - - +
71B TYR* 1.3 91.0 + + - +
74B TYR* 2.9 60.9 + + + +
75B ASN* 4.6 0.7 + - - -
81B LEU* 3.6 12.7 - - + +
82B TRP* 3.4 36.3 - + + -
98B VAL* 5.0 0.9 - - + -
102B THR* 3.6 34.8 + - + -
104B CYS* 3.8 15.7 - - + +
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Residues in contact with TYR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 3.4 36.0 - + - -
20B LEU* 3.3 36.3 - - + +
21B ILE* 4.0 21.1 - - + -
22B PRO* 3.5 22.7 - - + +
25B LEU* 3.4 30.7 - - + +
42B MSE 6.0 0.4 - - - -
67B LEU* 2.8 45.9 + - + +
68B CYS 4.4 1.1 - - - +
70B TYR* 1.3 100.1 - + - +
72B ALA* 1.3 56.6 + - - +
75B ASN* 3.8 0.7 + - - -
101B ILE 5.0 0.3 + - - -
102B THR* 3.6 19.9 - - - +
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Residues in contact with ALA 72 (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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20B LEU* 4.0 15.2 - - + +
42B MSE 3.6 39.8 - - + +
68B CYS 3.3 17.5 + - - +
69B LEU 2.8 3.3 + - - +
71B TYR* 1.3 78.8 - - - +
73B HIS* 1.3 73.6 + - + +
75B ASN* 4.0 11.0 + - - +
76B ARG* 5.4 1.6 - - - +
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Residues in contact with HIS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU 2.7 28.4 + - - -
42B MSE 3.8 11.1 + - - -
44B LEU 3.1 25.4 + - - -
45B SER* 4.4 0.7 - - - -
46B TYR* 3.5 47.6 + + + +
49B ALA* 3.9 5.3 - - - +
69B LEU* 2.8 32.3 + - + +
72B ALA* 1.3 87.2 + - + +
74B TYR* 1.3 65.1 + - - +
75B ASN* 2.9 5.4 + - - +
76B ARG* 2.9 21.0 + - + +
78B ALA* 3.3 14.8 - - - +
81B LEU* 5.7 1.6 - - + -
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Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 6.2 1.1 - + + -
237A GLU* 3.6 22.7 + - + -
69B LEU 4.1 0.4 + - - -
70B TYR* 2.9 53.5 + + + +
73B HIS* 1.3 76.7 - - - +
75B ASN* 1.3 62.5 + - - +
78B ALA 3.6 27.0 + - - +
79B LYS* 3.6 50.6 + - + +
81B LEU* 4.3 12.2 - - + +
82B TRP* 3.9 9.0 - + - -
104B CYS* 3.4 17.6 - - - -
106B SER* 3.0 29.1 + - - -
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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
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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