Contacts of the helix formed by residues 53 - 73 (chain A) 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 SER 53 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ASN* 4.6 1.2 - - - +
48A ASP* 2.5 41.7 + - - -
50A THR* 2.7 30.3 + - - -
52A GLY* 1.3 72.7 - - - +
54A PRO* 1.3 73.2 - - - +
55A HIS* 3.0 12.5 + - - +
56A ILE* 3.4 13.0 + - - +
57A LYS* 3.3 19.4 + - - +
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Residues in contact with PRO 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASP* 4.1 10.8 - - + +
52A GLY 4.1 4.0 - - - +
53A SER* 1.3 87.2 - - - +
55A HIS* 1.3 75.5 + - + +
57A LYS* 3.5 10.1 + - + +
58A ALA* 3.0 28.2 + - - +
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Residues in contact with HIS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TRP* 3.6 42.7 - + + -
47A PRO* 3.3 39.2 - - + +
48A ASP* 3.9 7.8 + - + +
53A SER* 3.0 11.3 + - - +
54A PRO* 1.3 90.9 - - + +
56A ILE* 1.3 61.3 - - - +
58A ALA* 3.5 4.9 + - - +
59A HIS* 3.0 31.4 + - - +
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Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASN* 3.4 22.3 - - - +
29A LEU* 3.4 22.7 - - + +
30A SER* 3.5 21.1 - - - +
33A ILE* 3.9 12.6 - - + -
46A TRP* 3.8 13.2 - - + -
49A VAL* 3.7 27.4 - - + -
50A THR 3.5 24.0 - - - +
51A PRO 4.6 1.3 - - - +
53A SER* 3.5 17.7 - - - +
55A HIS* 1.3 76.6 - - - +
57A LYS* 1.3 54.1 + - - +
59A HIS 3.4 0.3 + - - -
60A GLY* 2.8 31.4 + - - -
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Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASN* 3.2 28.7 + - + +
52A GLY 5.7 0.7 - - - +
53A SER 3.3 8.6 + - - +
54A PRO* 3.6 13.0 - - + +
55A HIS 3.2 0.2 - - - -
56A ILE* 1.3 77.2 - - - +
58A ALA* 1.3 62.7 + - - +
60A GLY* 3.3 6.8 + - - -
61A LYS* 2.9 43.0 + - + +
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PRO 3.0 16.7 + - - +
55A HIS* 3.9 6.5 - - - +
56A ILE 3.4 0.2 - - - -
57A LYS* 1.3 77.8 - - - +
59A HIS* 1.3 63.3 + - - +
61A LYS* 3.0 26.2 + - - +
62A LYS* 3.5 11.9 + - - +
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Residues in contact with HIS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.7 22.4 - - + -
43A PHE* 4.1 7.8 - + - -
46A TRP* 3.2 33.7 - + + -
55A HIS 3.0 9.8 + - - +
58A ALA* 1.3 74.9 - - - +
60A GLY* 1.3 59.9 + - - +
62A LYS* 2.8 41.7 + - + +
63A VAL* 2.8 44.0 + - + +
200A HEM 3.4 59.8 + + + +
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Residues in contact with GLY 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA 4.4 0.3 - - - +
22A ASP 4.4 2.0 - - - -
25A GLY* 3.4 41.3 - - - -
26A ASN 3.7 2.7 - - - -
29A LEU* 3.9 5.1 - - - +
56A ILE 2.8 16.9 + - - -
57A LYS 3.3 1.5 + - - -
58A ALA 3.3 0.6 - - - -
59A HIS* 1.3 76.0 - - - +
61A LYS* 1.3 60.6 + - - +
63A VAL* 3.5 4.1 + - - +
64A MET* 3.2 20.4 + - - +
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASP* 3.3 54.2 + - + +
57A LYS* 2.9 40.3 + - + +
58A ALA* 3.0 15.0 - - - +
60A GLY* 1.3 74.5 - - - +
62A LYS* 1.3 60.0 + - + +
64A MET* 3.9 1.4 - - - +
65A GLY* 2.9 25.1 + - - -
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Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TRP* 4.9 0.6 - - - -
58A ALA* 3.5 8.2 + - - +
59A HIS* 2.8 55.0 + - + +
61A LYS* 1.3 77.2 - - + +
63A VAL* 1.3 65.0 + - - +
65A GLY* 3.3 2.5 + - - -
66A GLY 3.0 17.5 + - - -
200A HEM 3.2 61.9 + - + +
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Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLY* 5.1 3.4 - - - -
28A ALA* 6.2 1.1 - - + -
29A LEU* 4.5 12.1 - - + -
59A HIS* 2.8 47.4 + - + +
60A GLY* 3.8 9.4 - - - +
61A LYS 3.4 0.2 - - - -
62A LYS* 1.3 73.3 - - - +
64A MET* 1.4 71.4 + - + +
66A GLY* 3.1 4.9 + - - -
67A ILE* 3.1 21.5 + - + +
102A LEU* 4.0 26.5 - - + -
106A ILE* 4.7 3.6 - - + -
200A HEM 3.6 33.8 - - + +
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Residues in contact with MET 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TRP* 3.8 31.3 - - + -
21A ALA* 3.1 41.7 - - + +
24A ILE* 3.6 25.1 - - + -
25A GLY* 3.3 21.3 - - - +
60A GLY 3.2 6.5 + - - +
61A LYS 4.4 1.8 - - - +
63A VAL* 1.4 75.8 - - - +
65A GLY* 1.3 61.2 + - - +
66A GLY 3.2 0.2 - - - -
67A ILE* 3.7 27.8 - - + +
68A ALA* 2.8 27.9 + - - +
106A ILE* 4.1 26.9 - - + -
110A ILE* 5.2 1.8 - - + -
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Residues in contact with GLY 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 6.1 0.2 - - - -
61A LYS 2.9 18.2 + - - -
62A LYS* 3.7 2.9 - - - -
63A VAL 3.2 0.2 - - - -
64A MET* 1.3 78.8 - - - +
66A GLY* 1.3 55.7 + - - +
68A ALA* 3.2 9.1 + - - +
69A LEU* 2.9 27.9 + - - +
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Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS 3.0 13.8 + - - -
63A VAL 3.1 6.2 + - - -
65A GLY* 1.3 73.6 - - - +
67A ILE* 1.3 58.5 + - - +
69A LEU* 3.3 9.6 + - - +
70A ALA* 2.9 27.2 + - - +
81A LEU* 4.3 5.7 - - - +
84A LEU* 4.3 13.7 - - - -
200A HEM 4.1 20.8 - - - +
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Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TRP* 4.4 12.3 - - + -
63A VAL* 3.1 16.3 + - + +
64A MET* 3.7 39.0 - - + +
65A GLY 3.3 0.4 - - - -
66A GLY* 1.3 72.4 - - - +
68A ALA* 1.3 66.7 + - - +
70A ALA* 3.0 5.6 + - - +
71A VAL* 2.9 26.0 + - + +
106A ILE* 4.2 8.7 - - + -
126A LEU* 6.2 1.6 - - + -
129A PHE* 4.4 13.0 - - + -
130A LEU* 3.9 24.5 - - + -
133A VAL* 4.4 12.3 - - + -
200A HEM 3.8 29.4 - - + -
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TRP* 3.8 31.1 + - + +
21A ALA* 6.0 0.2 - - + -
64A MET 2.8 17.6 + - - +
65A GLY* 3.2 9.4 + - - +
67A ILE* 1.3 76.1 - - - +
69A LEU* 1.3 63.3 + - - +
71A VAL* 3.1 5.7 + - - +
72A SER* 3.0 22.2 + - - -
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLY 2.9 14.2 + - - +
66A GLY* 3.4 8.3 - - - +
68A ALA* 1.3 77.6 - - - +
70A ALA* 1.3 64.4 + - - +
72A SER* 2.7 24.3 + - - +
73A LYS* 2.9 42.0 + - + +
80A GLY 4.0 9.9 - - - +
81A LEU* 3.9 19.5 - - + -
84A LEU* 4.4 14.8 - - + -
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLY 2.9 14.3 + - - +
67A ILE* 3.0 13.0 + - - +
69A LEU* 1.3 76.5 - - - +
71A VAL* 1.3 56.6 + - - +
73A LYS* 3.1 4.1 + - - +
74A ILE* 2.9 29.8 + - - -
77A LEU* 3.5 12.1 - - + +
81A LEU* 4.3 15.2 - - + +
129A PHE* 3.5 18.9 - - + -
133A VAL* 3.8 19.3 - - + -
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 4.1 14.4 - - + -
11A ARG* 4.2 29.0 + - + +
14A TRP* 3.9 44.9 - - + -
67A ILE* 2.9 21.5 + - + +
68A ALA 3.1 6.9 + - - +
70A ALA* 1.3 73.9 - - - +
72A SER* 1.3 64.1 + - - +
74A ILE* 3.3 21.9 - - + +
126A LEU* 6.2 0.2 - - + -
129A PHE* 3.8 21.1 - - + -
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Residues in contact with SER 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ARG* 5.0 5.3 + - - +
68A ALA 3.0 12.2 + - - -
69A LEU* 2.7 26.0 + - - +
71A VAL* 1.3 78.0 - - - +
73A LYS* 1.3 73.7 + - - +
74A ILE* 3.6 4.0 + - - +
75A ASP* 5.1 2.3 + - - +
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Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 2.9 44.1 + - + +
70A ALA* 3.3 7.4 - - - +
72A SER* 1.3 84.4 + - - +
74A ILE* 1.3 53.7 + - - +
75A ASP* 3.1 4.0 - - - -
76A ASP 2.8 34.5 + - - +
77A LEU* 3.4 5.2 + - + +
80A GLY* 3.8 32.8 - - - -
81A LEU* 5.6 0.2 - - + -
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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