Contacts of the helix formed by residues 50 - 67 (chain B) in PDB entry 2BNZ
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 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B THR* 3.5 16.1 - - - +
49B GLY* 1.3 76.2 - - - +
51B VAL* 1.3 64.5 + - - +
52B LYS* 3.5 14.0 + - - +
53B GLU* 3.2 54.9 + - - +
54B VAL* 3.9 3.5 - - - +
2E A 3.4 42.2 + - - +
3E A 3.4 5.2 - - - +
36H G 4.2 9.2 - - - +
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 4.4 10.1 - - + -
59A LEU* 6.6 0.2 - - + -
37B HIS* 3.4 36.8 - - + +
40B ILE* 4.1 17.7 - - + -
41B LYS* 3.6 42.0 - - + +
44B THR* 4.1 2.9 - - - +
50B ASN* 1.3 70.1 - - - +
52B LYS* 1.3 66.8 + - - +
54B VAL* 3.1 5.0 + - - +
55B MET* 3.1 24.3 + - + +
3E A 3.1 21.4 + - - +
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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
----------------------------------------------------------
30A VAL* 4.4 12.3 - - + +
31A ARG* 3.2 30.3 + - + +
32A VAL* 4.0 0.2 - - - +
33A ARG* 4.7 1.8 - - - +
27B ASP* 2.8 41.6 + - - -
50B ASN* 3.3 9.6 - - - +
51B VAL* 1.3 76.1 - - - +
53B GLU* 1.3 65.6 + - - +
54B VAL 3.0 0.3 + - - -
55B MET* 3.1 2.1 + - - +
56B ASP* 2.4 58.7 + - - +
2E A 3.4 40.2 - - + +
3E A 2.9 14.6 + - - +
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLY* 4.1 8.8 - - - -
50B ASN* 3.2 39.3 + - - +
51B VAL 3.3 0.2 - - - -
52B LYS* 1.3 80.5 - - - +
54B VAL* 1.3 64.1 - - + +
56B ASP* 3.7 7.8 + - - +
57B GLN* 3.2 22.7 + - - +
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 4.6 5.2 - - + -
62A TYR* 3.2 41.9 - - + +
40B ILE* 3.8 25.4 - - + -
44B THR* 4.0 17.9 - - + -
50B ASN 3.9 12.8 - - - +
51B VAL 3.1 7.3 + - - +
52B LYS 3.1 0.8 - - - -
53B GLU* 1.3 77.9 - - + +
55B MET* 1.3 55.0 + - - +
57B GLN* 3.1 8.8 + - - +
58B ALA* 2.7 32.4 + - - +
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Residues in contact with MET 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 3.6 34.8 - - + -
32A VAL* 4.3 9.9 - - + -
55A MET* 3.4 37.7 - - + +
58A ALA* 5.8 1.3 - - + -
59A LEU* 3.8 36.6 - - + -
32B VAL* 4.2 15.5 - - + -
37B HIS* 5.7 1.8 - - + -
40B ILE* 6.3 0.7 - - + -
51B VAL* 3.1 18.1 + - + +
52B LYS* 3.1 8.4 + - + +
54B VAL* 1.3 74.2 - - - +
56B ASP* 1.3 66.4 + - - +
58B ALA* 3.1 3.9 + - + +
59B LEU* 2.8 31.6 + - + +
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Residues in contact with ASP 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 3.4 9.2 - - - +
33A ARG* 2.9 47.5 + - + +
36A LEU* 3.9 5.7 - - - +
52B LYS* 2.4 48.3 + - - +
53B GLU* 3.8 6.6 + - - +
55B MET* 1.3 75.9 - - - +
57B GLN* 1.3 61.7 + - - +
59B LEU* 3.9 5.1 - - - +
60B GLU* 3.1 26.9 + - - +
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Residues in contact with GLN 57 (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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62A TYR* 3.0 30.8 + - + -
66A TYR* 4.4 6.5 + - - -
53B GLU 3.2 12.9 + - - +
54B VAL* 3.1 10.5 + - - +
55B MET 3.1 1.0 - - - -
56B ASP* 1.3 80.2 - - - +
58B ALA* 1.3 57.6 + - - +
60B GLU* 3.3 8.1 + - + +
61B GLU* 3.0 56.6 + - + +
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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
----------------------------------------------------------
58A ALA* 3.8 15.7 - - + +
59A LEU* 4.1 16.8 - - + -
62A TYR* 3.6 35.6 - - + -
54B VAL 2.7 20.0 + - - +
55B MET* 3.1 6.7 + - - +
57B GLN* 1.3 70.7 - - - +
59B LEU* 1.3 66.0 + - - +
61B GLU* 3.5 3.6 + - - +
62B TYR* 3.0 23.6 + - - +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 3.6 27.8 - - + -
36A LEU* 3.6 21.5 - - + -
37A HIS 4.3 3.4 - - - +
40A ILE* 3.6 20.2 - - + -
54A VAL* 4.8 5.2 - - + -
55A MET* 3.4 35.4 - - + -
58A ALA* 4.3 6.4 - - + +
55B MET* 2.8 20.2 + - + +
56B ASP 3.9 4.3 - - - +
58B ALA* 1.3 73.5 - - - +
60B GLU* 1.3 58.8 + - - +
62B TYR* 3.3 6.7 - - + +
63B ILE* 2.9 45.0 + - + +
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 5.5 3.6 - - - -
36A LEU* 4.2 18.3 - - + +
56B ASP 3.1 19.5 + - - +
57B GLN* 3.7 8.3 - - - +
59B LEU* 1.3 75.1 - - - +
61B GLU* 1.3 62.7 + - + +
63B ILE* 2.9 8.2 + - - +
64B ARG* 2.7 59.9 + - - +
71B LEU* 4.3 13.8 - - + +
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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
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62A TYR* 4.6 5.3 - - + -
65A LYS* 2.9 30.8 + - - +
66A TYR* 2.8 34.0 + - - -
57B GLN* 3.0 44.0 + - + +
58B ALA* 4.0 4.3 - - - +
60B GLU* 1.3 77.6 - - + +
62B TYR* 1.3 56.7 + - - +
64B ARG* 4.0 10.6 - - - +
65B LYS* 3.1 30.0 + - - +
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Residues in contact with TYR 62 (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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40A ILE* 4.0 15.0 - - + -
43A GLU* 6.1 0.9 - - + +
54A VAL* 3.7 42.5 - - + +
57A GLN* 3.8 21.9 + - + -
58A ALA* 3.6 29.6 - - + -
61A GLU* 4.3 5.6 - - - +
58B ALA 3.0 15.8 + - - +
59B LEU* 3.3 9.2 - - + +
61B GLU* 1.3 76.2 - - - +
63B ILE* 1.3 65.4 + - + +
65B LYS* 3.3 1.9 + - - -
66B TYR* 2.9 80.6 + + + +
67B LEU* 4.7 7.0 - - + -
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Residues in contact with ILE 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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36A LEU* 3.5 39.0 - - + +
39A ILE* 4.2 13.5 - - + -
40A ILE* 3.8 21.5 - - + -
59B LEU* 2.9 35.1 + - + +
60B GLU* 2.9 7.8 + - - +
62B TYR* 1.3 76.3 - - - +
64B ARG* 1.3 58.9 + - - +
67B LEU* 2.7 56.2 + - + +
71B LEU* 3.5 29.6 - - + +
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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
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60B GLU* 2.7 56.0 + - - +
61B GLU* 4.0 10.6 - - - +
63B ILE* 1.3 73.1 - - - +
65B LYS* 1.3 62.1 - - - +
68B PRO* 3.4 29.6 - - + +
71B LEU* 3.8 27.6 + - + +
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Residues in contact with LYS 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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61A GLU* 3.5 20.2 + - - +
61B GLU 3.1 18.9 + - - +
62B TYR* 3.7 4.3 - - - +
64B ARG* 1.3 79.6 - - - +
66B TYR* 1.3 99.7 + - + +
68B PRO* 4.4 3.9 - - - +
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Residues in contact with TYR 66 (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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57A GLN* 3.3 10.7 + - - -
61A GLU* 2.6 38.5 + - - -
62B TYR* 2.9 60.1 + + + +
65B LYS* 1.3 106.6 + - + +
67B LEU* 1.3 77.1 + - + +
68B PRO* 3.3 8.2 - - - +
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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
----------------------------------------------------------
39A ILE* 4.0 21.8 - - + -
40A ILE* 4.1 15.3 - - + -
43A GLU* 3.5 47.1 - - + +
62B TYR* 4.7 6.7 - - + -
63B ILE* 2.7 31.0 + - + +
66B TYR* 1.3 87.2 - - + +
68B PRO* 1.3 66.2 - - - +
69B ASP* 3.2 7.6 - - - -
70B LYS* 2.9 35.9 + - + +
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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
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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