Contacts of the helix formed by residues 57 - 77 (chain B) in PDB entry 2PEG
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 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B PHE 4.6 8.7 + - - -
53B ALA 3.0 16.3 + - - +
54B ILE* 3.1 13.6 + - - +
55B ILE 4.9 0.9 - - - +
56B GLY* 1.3 75.8 - - - +
58B ALA* 1.3 57.0 + - - +
59B ASN* 2.7 44.2 + - - +
60B VAL* 2.9 24.9 + - + +
61B ALA* 3.0 26.4 + - - +
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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
----------------------------------------------------------
56B GLY 3.2 7.2 + - - +
57B ASN* 1.3 69.1 + - - +
59B ASN* 1.3 62.8 + - - +
61B ALA* 3.7 8.6 - - - +
62B ALA* 2.9 30.0 + - - +
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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
----------------------------------------------------------
42B PHE* 4.4 20.3 + - + +
57B ASN* 2.7 22.6 + - - +
58B ALA* 1.3 74.4 - - - +
60B VAL* 1.3 65.5 + - - +
62B ALA* 3.3 6.4 + - - +
63B HIS* 3.2 23.6 + - - +
400B HEM 5.0 1.7 - - - +
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PRO* 4.6 1.3 - - - +
28B LEU* 3.1 34.3 - - + +
29B SER* 3.4 30.7 - - - +
32B LEU* 3.6 24.2 - - + -
42B PHE* 3.9 16.8 - - + -
54B ILE* 4.1 7.4 - - + +
55B ILE 5.9 0.2 - - - +
57B ASN* 2.9 34.0 + - + +
59B ASN* 1.3 78.0 - - - +
61B ALA* 1.3 63.5 + - - +
64B GLY* 3.0 18.5 + - - -
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PRO* 3.6 31.4 - - + +
55B ILE 5.9 2.2 - - - +
56B GLY 5.8 0.7 - - - +
57B ASN 3.0 12.7 + - - +
58B ALA* 3.7 12.3 - - - +
59B ASN 3.2 0.2 - - - -
60B VAL* 1.3 78.6 - - - +
62B ALA* 1.3 63.2 + - - +
64B GLY 3.3 0.9 + - - -
65B ILE* 3.0 32.8 + - + +
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Residues in contact with ALA 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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58B ALA 2.9 18.4 + - - +
59B ASN* 3.7 7.4 - - - +
60B VAL 3.3 0.2 - - - -
61B ALA* 1.3 75.4 - - - +
63B HIS* 1.3 62.6 + - - +
65B ILE* 3.3 9.9 + - - +
66B LYS* 3.0 34.4 + - - +
400B HEM 5.5 1.6 - - - +
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Residues in contact with HIS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.3 22.9 - - + +
42B PHE* 3.3 21.3 - + + -
59B ASN 3.2 9.5 + - - +
62B ALA* 1.3 76.0 - - - +
64B GLY* 1.3 60.8 + - - +
66B LYS* 3.1 6.6 + - + +
67B VAL* 2.8 49.4 + - + +
400B HEM 2.0 109.9 + + + +
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Residues in contact with GLY 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLY* 3.3 39.0 - - - -
28B LEU* 3.7 11.8 - - - +
60B VAL 3.0 14.3 + - - -
61B ALA 3.3 2.8 + - - -
63B HIS* 1.3 76.2 - - - +
65B ILE* 1.3 61.4 + - - +
67B VAL* 3.4 10.1 + - - +
68B LEU* 3.4 15.9 + - - +
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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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20B TYR* 3.7 14.1 - - + +
21B ASP* 3.5 33.4 - - - +
25B PRO* 3.6 25.1 - - + -
61B ALA* 3.0 22.0 + - + +
62B ALA* 3.7 7.2 - - - +
64B GLY* 1.3 74.4 - - - +
66B LYS* 1.3 64.6 + - - +
68B LEU* 3.2 5.6 + - - +
69B HIS* 3.1 40.5 + - + +
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Residues in contact with LYS 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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62B ALA* 3.0 25.0 + - - +
63B HIS* 3.1 8.5 + - - +
65B ILE* 1.3 77.9 - - + +
67B VAL* 1.3 57.5 + - - +
69B HIS* 3.3 7.0 + - - +
70B GLY* 2.8 27.4 + - - -
400B HEM 2.7 84.9 + - + +
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Residues in contact with VAL 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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28B LEU* 5.5 1.1 - - + -
63B HIS* 2.8 52.7 + - + +
64B GLY* 3.5 11.9 - - - +
65B ILE 3.2 0.4 - - - -
66B LYS* 1.3 73.2 - - - +
68B LEU* 1.3 66.0 + - + +
70B GLY* 3.1 3.5 + - - -
71B LEU* 3.0 22.7 + - + +
106B LEU* 4.3 9.2 - - + -
110B ILE* 4.1 21.1 - - + -
400B HEM 3.6 45.2 - - + +
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Residues in contact with LEU 68 (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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15B PHE* 4.4 3.2 - - + -
18B MET* 4.9 7.2 - - - -
20B TYR* 3.6 49.7 + - + +
23B ILE* 3.9 14.1 - - + -
24B GLY* 3.2 36.6 - - - +
27B ALA* 5.5 1.8 - - + -
64B GLY 3.4 6.7 + - - +
65B ILE 3.2 8.5 + - - +
67B VAL* 1.3 87.8 - - + +
69B HIS* 1.3 65.6 + - - +
71B LEU* 3.2 26.8 + - + +
72B ASP* 3.3 8.7 + - - +
110B ILE* 4.5 18.8 - - + -
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Residues in contact with HIS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.4 31.7 - + + +
21B ASP* 5.2 1.6 + - - -
65B ILE* 3.1 46.3 + - + +
66B LYS* 3.9 6.3 - - - +
68B LEU* 1.3 75.5 - - - +
70B GLY* 1.3 63.9 + - - +
72B ASP* 3.1 22.9 + - - +
73B ARG* 3.8 5.7 + - - +
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Residues in contact with GLY 70 (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 2.8 16.2 + - - -
67B VAL 3.1 6.7 + - - -
69B HIS* 1.3 78.7 - - - +
71B LEU* 1.3 51.8 + - - +
73B ARG* 3.3 27.0 - - - +
85B TYR* 2.5 34.2 + - - -
88B LEU* 5.0 0.4 - - - -
400B HEM 4.2 14.6 - - - -
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Residues in contact with LEU 71 (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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15B PHE* 3.7 23.3 - - + -
67B VAL* 3.0 19.9 + - + +
68B LEU* 3.2 19.9 + - + +
70B GLY* 1.3 75.1 - - - +
72B ASP* 1.3 60.7 + - - +
74B GLY* 2.9 17.2 + - - -
75B VAL* 3.0 15.1 + - - +
85B TYR* 3.3 4.1 + - - +
110B ILE* 4.1 21.8 - - + -
133B PHE* 3.5 4.8 - - + -
134B LEU* 3.9 29.4 - - + -
137B VAL* 3.8 32.8 - - + -
400B HEM 4.3 12.1 - - + -
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Residues in contact with ASP 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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15B PHE* 4.1 9.0 - - - +
20B TYR* 3.1 30.0 + - - -
68B LEU 3.3 7.7 + - - +
69B HIS* 3.1 21.0 + - - +
71B LEU* 1.3 79.3 - - - +
73B ARG* 1.3 56.1 + - - +
75B VAL* 3.1 17.5 + - - +
76B LYS* 2.9 31.9 + - - +
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Residues in contact with ARG 73 (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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69B HIS 3.8 4.3 + - - +
70B GLY* 3.3 26.3 + - - +
72B ASP* 1.3 78.0 - - - +
74B GLY* 1.3 64.4 + - - +
76B LYS* 3.5 8.0 + - - +
77B ASN* 3.0 32.6 + - - +
84B THR* 3.3 38.0 + - + -
85B TYR* 3.6 5.6 - - - +
87B ASP* 6.3 0.6 - - - +
88B LEU* 4.1 29.6 - - - +
400B HEM 4.6 8.5 - - - +
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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
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71B LEU 2.9 9.7 + - - -
73B ARG* 1.3 78.7 - - - +
75B VAL* 1.3 62.6 + - - +
77B ASN* 3.2 27.9 - - - +
78B MET* 3.3 8.3 + - - +
81B ILE* 4.1 4.6 - - - +
85B TYR* 3.1 27.2 + - - -
133B PHE* 3.7 12.0 - - - -
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Residues in contact with VAL 75 (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* 3.9 15.5 - - + -
12B SER* 4.7 11.4 - - - -
15B PHE* 3.6 40.8 - - + -
71B LEU 3.0 12.9 + - - +
72B ASP* 3.1 17.0 + - - +
74B GLY* 1.3 77.5 - - - +
76B LYS* 1.3 62.1 + - + +
77B ASN 3.5 0.3 + - - -
78B MET* 3.7 20.9 + - - +
133B PHE* 3.6 15.0 - - + -
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Residues in contact with LYS 76 (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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72B ASP* 2.9 15.2 + - - +
73B ARG* 3.6 13.0 - - - +
74B GLY 3.2 0.2 - - - -
75B VAL* 1.3 78.3 - - + +
77B ASN* 1.3 62.5 + - - +
78B MET 3.9 0.2 - - - -
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Residues in contact with ASN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ARG* 3.0 22.2 + - - +
74B GLY* 3.2 7.4 + - - +
76B LYS* 1.3 82.5 - - - +
78B MET* 1.3 58.0 + - - +
79B ASP 3.0 5.6 - - - +
80B ASN* 3.0 30.4 + - + +
81B ILE* 3.8 3.5 - - - +
84B THR* 2.8 32.2 + - - +
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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