Contacts of the helix formed by residues 57 - 76 (chain B) in PDB entry 1I3D
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
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PHE 2.9 23.9 + - - +
46B GLY* 4.4 2.0 - - - -
47B ASN 3.8 18.2 + - - +
48B LEU* 3.9 6.1 - - - +
53B ALA 3.1 10.3 + - - +
54B ILE* 3.0 16.6 + - - +
55B MET 3.5 0.5 - - - +
56B GLY* 1.3 76.6 - - - +
58B PRO* 1.3 70.8 - - - +
59B LYS* 2.7 37.2 + - - +
60B VAL* 3.1 20.5 + - + +
61B LYS* 3.2 22.6 + - - -
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Residues in contact with PRO 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLY 3.3 9.1 - - - +
57B ASN* 1.3 87.3 - - - +
59B LYS* 1.3 64.5 + - + +
61B LYS* 3.4 12.7 + - + +
62B ALA* 3.0 29.6 + - - +
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Residues in contact with LYS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B SER* 2.8 28.7 + - - -
45B PHE* 3.6 41.1 - - + +
57B ASN* 2.7 14.2 + - - +
58B PRO* 1.3 76.9 - - + +
60B VAL* 1.3 61.3 + - - +
62B ALA* 3.8 5.5 - - - +
63B HIS* 2.8 31.9 + - - +
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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 GLY* 4.1 7.4 - - - +
28B LEU* 3.6 14.6 - - + +
29B GLY* 3.9 32.1 - - - +
32B LEU* 4.0 18.6 - - + -
45B PHE* 4.0 16.2 - - + -
48B LEU* 4.1 9.0 - - + -
54B ILE 3.9 11.2 - - - +
55B MET* 5.7 0.9 - - - +
57B ASN* 3.1 29.8 + - + +
59B LYS* 1.3 79.1 - - - +
61B LYS* 1.3 58.3 + - - +
64B GLY* 2.8 27.5 + - - -
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLU* 4.3 23.6 - - - +
22B ASP* 5.4 5.6 - - - +
25B GLY* 3.8 20.9 + - - -
55B MET 4.1 15.8 + - - -
56B GLY* 4.9 3.6 - - - -
57B ASN 3.2 14.3 + - - +
58B PRO* 3.7 15.3 - - - +
59B LYS 3.3 0.2 - - - -
60B VAL* 1.3 80.8 - - - +
62B ALA* 1.3 61.9 + - - +
64B GLY* 3.4 1.2 + - - -
65B LYS* 3.1 22.0 + - - +
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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
----------------------------------------------------------
58B PRO 3.0 17.5 + - - +
59B LYS* 4.0 6.5 - - - +
61B LYS* 1.3 77.0 - - - +
63B HIS* 1.4 64.4 + - - +
65B LYS* 3.4 19.8 + - - +
66B LYS* 3.5 18.7 + - - +
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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* 3.6 17.3 - - + -
42B PHE* 4.0 8.6 - + - -
45B PHE* 3.6 21.0 - + + -
59B LYS 2.8 19.0 + - - +
62B ALA* 1.4 72.3 - - - +
64B GLY* 1.3 68.6 + - - +
65B LYS 3.0 1.3 - - - -
66B LYS* 2.9 30.6 + - + +
67B VAL* 3.1 13.0 + - + +
147B HEM 3.3 54.6 - + + +
148B CMO 3.0 34.5 - - - -
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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 38.6 - - - -
28B LEU* 3.8 10.9 - - - +
60B VAL 2.8 15.1 + - - -
61B LYS 3.9 0.2 - - - -
63B HIS* 1.3 78.2 - - - +
65B LYS* 1.3 62.6 + - - +
67B VAL* 3.3 9.3 + - - +
68B LEU 3.1 19.6 + - - -
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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
----------------------------------------------------------
20B VAL* 3.6 23.2 - - - +
21B GLU* 3.6 38.3 + - - +
24B GLY* 4.2 4.9 - - - -
25B GLY 5.3 0.2 - - - +
61B LYS 3.1 13.2 + - - +
62B ALA* 3.5 13.9 - - - +
63B HIS 3.0 1.0 - - - -
64B GLY* 1.3 79.0 - - - +
66B LYS* 1.4 59.1 + - + +
68B LEU 3.5 0.3 + - - -
69B THR* 2.7 40.8 + - - +
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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
----------------------------------------------------------
62B ALA* 3.6 19.1 - - - +
63B HIS* 2.9 25.7 + - - +
65B LYS* 1.4 79.3 - - + +
67B VAL* 1.4 61.9 + - + +
69B THR* 3.3 6.4 + - - -
70B SER* 2.9 29.4 + - - -
147B HEM 3.9 40.1 + - + +
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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
----------------------------------------------------------
27B THR* 6.5 0.2 - - + -
28B LEU* 5.2 2.7 - - + -
63B HIS* 3.1 23.3 + - + +
64B GLY* 3.5 9.9 - - - +
66B LYS* 1.4 76.2 - - - +
68B LEU* 1.4 70.0 + - + +
70B SER* 3.3 2.9 + - - -
71B LEU* 3.0 25.1 + - + +
106B LEU* 4.3 11.9 - - + -
147B HEM 3.7 47.2 - - + +
148B CMO 3.3 31.0 - - - +
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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
----------------------------------------------------------
15B TRP* 3.2 30.7 - - + -
18B VAL* 4.6 2.7 - - + -
20B VAL* 3.6 18.8 - - + -
23B ALA* 3.6 20.0 - - + +
24B GLY* 3.3 36.3 - - - +
27B THR* 4.5 15.5 - - + -
64B GLY 3.1 9.8 + - - +
67B VAL* 1.4 90.7 - - + +
69B THR* 1.4 59.6 + - - +
71B LEU* 3.5 9.6 - - + +
72B GLY 2.8 23.4 + - - -
110B LEU* 4.5 15.9 - - + -
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Residues in contact with THR 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 3.6 14.8 - - - +
65B LYS* 2.7 33.6 + - - +
66B LYS* 3.7 6.7 - - - -
68B LEU* 1.4 77.2 - - - +
70B SER* 1.4 59.9 + - - +
72B GLY* 3.2 2.2 + - - +
73B ASP* 3.0 26.9 + - + +
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Residues in contact with SER 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LYS 2.9 17.5 + - - -
67B VAL 3.6 4.3 - - - -
69B THR* 1.4 72.7 - - - +
71B LEU* 1.3 64.7 + - - +
73B ASP* 3.3 8.1 + - - +
74B ALA* 3.1 22.2 + - - +
84B THR* 5.8 0.3 - - - +
85B PHE* 4.4 5.6 - - - -
88B LEU* 4.2 13.3 - - - +
147B HEM 3.4 30.5 - - - +
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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
----------------------------------------------------------
15B TRP* 3.8 18.2 - - + -
67B VAL* 3.0 14.7 + - + +
68B LEU* 3.5 13.0 - - + +
69B THR 3.3 0.2 - - - -
70B SER* 1.3 73.3 - - - +
72B GLY* 1.3 67.3 + - - +
74B ALA* 3.0 6.8 + - + +
75B ILE* 3.0 34.1 + - + +
85B PHE* 4.4 8.1 - - + -
110B LEU* 3.4 32.3 - - + -
130B TRP* 4.9 4.0 - - + -
133B MET* 4.2 8.7 - - + -
137B VAL* 3.7 37.7 - - + -
147B HEM 4.6 13.4 - - + +
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Residues in contact with GLY 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 3.2 36.0 + - - -
68B LEU 2.8 13.3 + - - -
69B THR* 3.7 2.7 - - - -
70B SER 3.2 0.4 - - - -
71B LEU* 1.3 80.3 - - - +
73B ASP* 1.4 59.4 + - - +
75B ILE* 3.3 16.4 + - - +
76B LYS* 3.7 16.2 + - - +
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Residues in contact with ASP 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B THR* 3.0 14.6 + - + +
70B SER* 3.6 10.8 - - - +
71B LEU 3.2 0.4 - - - -
72B GLY* 1.4 75.4 - - - +
74B ALA* 1.3 56.6 + - - +
76B LYS* 2.9 49.1 + - - +
77B HIS* 3.2 22.9 + - - -
84B THR* 4.3 9.2 - - - +
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B SER 3.1 7.5 + - - +
71B LEU 3.0 8.4 + - - +
73B ASP* 1.3 76.9 + - - +
75B ILE* 1.3 58.7 + - - +
76B LYS 3.0 0.7 - - - -
77B HIS* 2.9 28.2 + - - -
78B LEU 3.5 0.5 + - - -
81B LEU* 3.4 15.0 - - + +
84B THR* 4.1 16.5 - - + +
85B PHE* 3.4 40.6 - - + -
133B MET* 5.0 3.4 - - + -
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Residues in contact with ILE 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* 3.8 27.8 - - + -
12B THR* 4.2 24.3 + - + +
15B TRP* 3.5 46.7 - - + -
71B LEU* 3.0 21.5 + - + +
72B GLY 3.5 10.8 - - - +
73B ASP 3.1 0.6 - - - -
74B ALA* 1.3 77.0 - - - +
76B LYS* 1.4 59.2 + - + +
77B HIS 3.3 0.2 - - - -
78B LEU* 3.4 23.1 - - + +
130B TRP* 3.9 7.0 - - + -
133B MET* 3.6 20.4 - - + -
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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
----------------------------------------------------------
72B GLY 3.7 18.1 + - - +
73B ASP* 2.9 32.2 + - - +
75B ILE* 1.4 79.0 - - + +
77B HIS* 1.3 70.7 + - + +
78B LEU 3.7 1.3 - - - -
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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
------------------------------------------------------------
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