Contacts of the helix formed by residues 49 - 67 (chain B) in PDB entry 2I91
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 GLU 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B GLY 5.1 4.2 - - - +
44B GLY* 4.3 0.2 - - - -
45B THR 6.0 0.4 - - - -
47B TYR 4.0 2.9 + - - +
48B ILE* 1.3 76.0 - - - +
50B GLU* 1.3 76.1 + - - +
51B LYS* 4.7 4.9 - - + +
52B LYS* 3.1 12.6 + - + +
53B LEU* 3.0 18.5 + - - +
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Residues in contact with GLU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B SER* 2.9 27.6 - - - +
42B GLU* 3.0 12.7 - - - +
43B GLY* 2.7 24.6 + - - +
44B GLY* 3.7 14.2 - - - +
48B ILE 3.7 2.0 + - - -
49B GLU* 1.3 78.6 + - - +
51B LYS* 1.3 64.1 + - - +
53B LEU* 3.0 12.3 + - - +
54B GLY* 3.1 11.1 + - - -
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 3.3 4.4 - - + +
50B GLU* 1.3 79.2 + - - +
52B LYS* 1.3 65.0 + - + +
54B GLY* 3.2 4.5 + - - -
55B GLN* 3.1 42.9 + - + +
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Residues in contact with LYS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ILE* 4.2 12.7 - - + +
49B GLU* 3.1 14.0 + - + +
51B LYS* 1.3 76.7 - - + +
53B LEU* 1.3 60.8 + - - +
55B GLN* 3.6 18.8 - - + +
56B GLU* 2.8 51.7 + - + +
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ARG* 3.9 9.2 - - - +
40B GLY 4.3 0.7 - - - +
41B SER* 3.9 15.9 - - - -
44B GLY* 3.4 31.0 - - - -
45B THR* 3.9 11.9 - - + -
48B ILE* 3.9 15.9 - - + +
49B GLU 3.0 10.8 + - - +
50B GLU 3.0 10.7 + - - +
52B LYS* 1.3 74.0 - - - +
54B GLY* 1.3 60.1 + - - +
56B GLU* 3.3 3.7 + - - +
57B ASN* 2.6 58.9 + - - +
503B SER* 3.4 33.2 - - - +
504B ASN* 4.2 5.2 - - - +
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Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PHE* 5.5 1.3 - - - -
41B SER* 3.8 18.7 - - - -
50B GLU 3.1 9.2 + - - -
51B LYS 3.7 3.4 - - - -
53B LEU* 1.3 81.0 - - - +
55B GLN* 1.3 50.4 + - - +
57B ASN* 3.2 5.5 + - - +
58B ALA* 2.7 37.0 + - - +
94B PHE* 5.7 2.1 - - - -
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Residues in contact with GLN 55 (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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51B LYS* 3.1 35.4 + - + +
52B LYS* 3.6 24.9 - - + +
53B LEU 3.2 0.2 - - - -
54B GLY* 1.3 74.5 - - - +
56B GLU* 1.3 64.9 + - - +
58B ALA* 3.7 6.5 - - - +
59B GLU* 3.0 36.0 + - + +
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Residues in contact with GLU 56 (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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32B ARG* 2.7 52.0 + - - +
48B ILE* 3.9 27.3 - - - +
52B LYS* 2.8 48.3 + - + +
53B LEU* 3.6 3.1 - - - +
55B GLN* 1.3 75.8 - - + +
57B ASN* 1.3 62.7 + - - +
59B GLU* 3.5 16.6 + - - +
60B ALA* 3.3 16.8 + - - +
63B ARG* 5.0 0.9 + - - -
505B GLY 4.3 4.7 + - - -
506B PHE* 5.5 5.5 - - - -
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Residues in contact with ASN 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ARG* 3.5 18.3 + - - +
36B PHE* 3.5 52.9 - - + +
41B SER* 4.9 0.3 - - - -
53B LEU* 2.6 45.8 + - - +
54B GLY* 3.6 4.2 - - - +
56B GLU* 1.3 76.0 - - - +
58B ALA* 1.3 64.8 + - - +
60B ALA* 3.4 6.4 + - - +
61B LEU* 3.1 21.0 + - - +
503B SER* 3.3 21.1 + - - +
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Residues in contact with ALA 58 (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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54B GLY 2.7 20.5 + - - +
55B GLN* 3.3 8.3 + - - +
57B ASN* 1.3 72.7 - - - +
59B GLU* 1.3 63.9 + - + +
61B LEU* 3.1 9.2 + - - +
62B LEU* 2.9 36.2 + - + +
94B PHE* 5.0 19.1 - - + -
98B VAL* 6.3 1.6 - - + -
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Residues in contact with GLU 59 (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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55B GLN* 3.0 30.5 + - + +
56B GLU* 3.6 18.8 - - - +
58B ALA* 1.3 79.0 - - + +
60B ALA* 1.3 57.3 + - - +
62B LEU* 3.4 9.1 + - + +
63B ARG* 2.9 47.3 + - - +
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Residues in contact with ALA 60 (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 ASP* 3.8 16.3 - - + +
32B ARG* 4.3 21.1 - - + -
56B GLU 3.3 10.8 + - - +
57B ASN* 3.8 7.2 - - - +
58B ALA 3.3 0.4 - - - -
59B GLU* 1.3 75.3 - - - +
61B LEU* 1.3 68.4 + - - +
63B ARG* 3.2 28.8 + - - +
64B LEU* 3.1 25.3 + - - +
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 4.8 9.2 - - + -
36B PHE* 5.7 4.7 - - + -
57B ASN 3.1 13.1 + - - +
58B ALA* 3.1 13.0 + - - +
60B ALA* 1.3 76.9 - - - +
62B LEU* 1.3 64.0 + - + +
64B LEU* 2.9 33.0 + - + +
65B ILE* 3.3 15.5 + - + +
73B VAL* 3.9 27.4 - - + -
94B PHE* 5.6 3.4 - - + -
95B ALA* 4.0 26.5 - - + +
98B VAL* 4.0 35.4 - - + -
99B CYS* 4.5 2.2 - - - -
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ALA* 2.9 35.2 + - + +
59B GLU* 3.8 7.6 - - - +
61B LEU* 1.3 78.7 - - - +
63B ARG* 1.3 57.7 + - - +
65B ILE* 3.2 14.8 + - + +
66B GLU* 2.8 35.9 + - - +
98B VAL* 4.7 19.7 - - + -
102B CYS* 6.0 4.5 - - + -
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Residues in contact with ARG 63 (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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26B GLN* 4.0 17.3 + - - -
29B ASP* 2.9 36.1 + - - +
32B ARG* 5.3 4.0 - - - +
56B GLU 5.0 1.6 + - - -
59B GLU* 2.9 43.1 + - - +
60B ALA* 3.3 27.1 - - - +
62B LEU* 1.3 76.3 - - - +
64B LEU* 1.3 58.9 + - - +
66B GLU* 2.9 22.3 - - + +
67B ASP* 2.6 32.7 + - - +
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Residues in contact with LEU 64 (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 ASP* 3.4 33.2 - - + +
30B MET* 3.9 25.8 - - + +
33B LEU* 4.5 9.0 - - + -
60B ALA 3.1 18.0 + - - +
61B LEU* 2.9 17.7 + - + +
63B ARG* 1.3 75.5 - - - +
65B ILE* 1.3 60.4 + - - +
67B ASP* 3.1 11.2 + - - +
69B LYS* 2.8 51.8 + - + +
73B VAL* 3.3 27.8 - - + -
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Residues in contact with ILE 65 (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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61B LEU* 3.7 30.1 - - + +
62B LEU* 3.2 16.8 + - + +
64B LEU* 1.3 72.5 - - + +
66B GLU* 1.3 70.4 + - - +
68B GLY* 2.9 15.6 + - - -
70B GLY* 4.1 17.8 + - - +
73B VAL* 5.5 1.1 - - + -
98B VAL* 4.6 6.7 - - + -
99B CYS* 4.5 13.5 - - - -
102B CYS* 3.4 46.4 - - + -
103B SER* 4.4 7.2 - - - +
104B ASP* 4.1 21.8 - - + +
107B THR* 4.7 3.4 - - + +
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Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 2.8 17.6 + - - +
63B ARG* 2.9 21.3 - - + +
65B ILE* 1.3 78.3 - - - +
67B ASP* 1.3 64.8 + - - +
68B GLY* 3.1 3.8 + - - -
103B SER* 4.6 10.3 + - - -
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Residues in contact with ASP 67 (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 ASP* 4.8 3.3 - - - +
63B ARG* 2.6 33.5 + - - +
64B LEU* 3.1 6.7 + - - +
66B GLU* 1.3 79.8 - - - +
68B GLY* 1.3 54.8 + - - +
69B LYS* 3.3 20.0 + - + +
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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
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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