Contacts of the helix formed by residues 57 - 75 (chain B) in PDB entry 4H7Y
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
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13B PRO* 3.4 19.1 - - - +
14B GLU* 2.9 24.0 + - - +
54B TYR* 2.9 32.2 + - + +
55B GLY 3.4 0.5 - - - +
56B GLN* 1.3 77.9 - - - +
58B GLU* 1.3 62.7 + - - +
59B SER* 2.9 19.1 + - - -
60B PHE* 2.9 29.2 + - + +
61B ALA* 3.0 21.7 + - - +
90B CYS* 5.5 0.2 - - - -
93B PHE* 3.8 1.9 - - - -
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLN 3.5 4.4 + - - -
57B ASN* 1.3 74.2 + - - +
59B SER* 1.3 56.9 + - - +
61B ALA* 3.2 2.6 + - - +
62B ARG* 2.9 62.4 + - - +
93B PHE* 3.6 32.6 - - + -
95B PHE* 4.1 19.3 - - + -
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Residues in contact with SER 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO* 3.8 26.0 - - - -
14B GLU* 3.7 19.3 + - - +
17B LEU* 3.8 18.7 - - - +
57B ASN* 2.9 9.2 + - - -
58B GLU* 1.3 74.1 - - - +
60B PHE* 1.3 60.3 + - - +
62B ARG* 3.2 17.6 + - - +
63B ILE* 2.9 31.4 + - - +
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Residues in contact with PHE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO* 3.5 8.6 - - + +
46B ILE* 5.6 4.3 - - + -
49B LEU* 3.3 50.9 - - + -
51B PRO* 3.9 26.5 - - + -
54B TYR* 3.2 38.1 - + + +
57B ASN* 2.9 17.0 + - - +
59B SER* 1.3 77.0 - - - +
61B ALA* 1.3 61.6 + - - +
63B ILE* 3.2 8.7 + - + +
64B GLN* 3.1 53.1 + - + +
89B ASN* 4.1 7.0 - - + -
90B CYS* 3.8 23.3 - - - -
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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
----------------------------------------------------------
57B ASN 3.0 9.7 + - - +
58B GLU 3.2 9.1 + - - +
60B PHE* 1.3 77.3 - - - +
62B ARG* 1.3 57.8 + - - +
64B GLN* 3.4 1.7 + - - +
65B VAL* 3.0 33.3 + - - +
90B CYS* 3.6 24.5 - - + -
93B PHE* 3.6 29.8 - - + -
95B PHE* 3.6 13.5 - - + -
96B VAL* 4.0 2.4 - - + +
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Residues in contact with ARG 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 3.6 28.2 - - + +
21B LEU* 6.3 0.2 - - - -
58B GLU* 2.9 50.7 + - - +
59B SER* 3.5 32.7 + - - +
61B ALA* 1.3 75.2 - - - +
63B ILE* 1.3 58.8 + - - +
65B VAL* 4.0 1.0 - - - +
66B ARG* 2.9 38.2 + - + +
95B PHE* 3.7 22.5 - - + -
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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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13B PRO* 3.7 24.0 - - + +
16B TRP* 3.9 11.7 - - + -
17B LEU* 4.0 11.4 - - + +
20B LEU* 4.0 12.1 - - + -
42B TYR* 3.6 24.5 - - + +
45B ALA* 4.1 12.3 - - + -
46B ILE* 4.0 21.8 - - + +
49B LEU* 3.8 24.2 - - + -
59B SER 2.9 21.3 + - - +
60B PHE* 3.2 9.8 + - + +
62B ARG* 1.3 77.9 - - - +
64B GLN* 1.3 63.5 + - + +
66B ARG 3.4 0.2 + - - -
67B PHE* 3.0 21.1 + - - +
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Residues in contact with GLN 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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46B ILE* 4.0 26.4 - - + +
60B PHE* 3.1 46.2 + - + +
61B ALA 3.8 2.9 - - - +
63B ILE* 1.3 76.1 - - + +
65B VAL* 1.3 62.2 + - - +
67B PHE* 3.4 3.8 + - - +
68B ALA* 3.1 22.3 + - - +
85B MET* 3.7 13.6 - - + +
86B ALA* 3.5 30.8 + - + +
89B ASN* 2.9 23.0 + - - +
90B CYS* 4.1 4.9 - - - -
81C ASP* 3.1 25.1 + - - -
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Residues in contact with VAL 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 ALA 3.0 20.6 + - - +
62B ARG 4.0 2.7 - - - +
64B GLN* 1.3 73.5 - - - +
66B ARG* 1.3 62.7 + - + +
68B ALA* 3.2 6.9 + - - +
69B GLU* 2.8 52.7 + - - +
83B PHE* 6.1 0.7 - - + -
86B ALA* 4.4 5.8 - - + -
95B PHE* 3.7 26.2 - - + -
96B VAL* 3.8 29.8 - - + -
99B SER* 3.4 17.3 - - - +
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Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PRO* 3.4 24.9 + - - +
30A LEU 3.0 31.1 + - - +
31A SER* 4.8 1.6 - - - +
17B LEU* 5.3 2.0 - - + -
21B LEU* 5.3 4.7 - - + -
24B GLU* 2.9 36.3 + - - -
42B TYR* 3.4 29.4 - - + +
62B ARG* 2.9 26.1 + - + +
65B VAL* 1.3 78.0 - - + +
67B PHE* 1.3 58.0 + - - +
69B GLU* 2.9 36.6 + - - +
70B LEU* 2.9 57.2 + - - +
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Residues in contact with PHE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 3.6 30.5 - - + -
42B TYR* 3.7 27.1 - - + -
43B SER* 3.9 15.5 - - - -
46B ILE* 3.7 20.2 - - + -
63B ILE 3.0 16.7 + - - +
64B GLN 3.6 4.5 - - - +
65B VAL 3.2 0.2 - - - -
66B ARG* 1.3 76.6 - - - +
68B ALA* 1.3 64.2 + - - +
70B LEU* 3.3 5.0 + - - +
71B LYS* 2.9 47.2 + - + +
82B TYR* 3.5 33.9 - + + -
85B MET* 4.4 3.4 - - + -
85C MET* 3.7 18.6 - - + -
88C ALA* 4.0 16.6 - - + -
89C ASN* 5.6 0.2 - - - -
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Residues in contact with ALA 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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64B GLN 3.1 12.1 + - - +
65B VAL* 3.6 9.0 - - - +
67B PHE* 1.3 80.3 - - - +
69B GLU* 1.3 55.7 + - - +
71B LYS* 3.3 3.5 + - - +
72B ALA 2.9 23.7 + - - -
79B ALA* 4.4 0.2 - - - +
82B TYR* 3.7 35.0 - - + +
83B PHE* 3.5 37.9 - - + +
86B ALA* 5.1 0.7 - - + -
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Residues in contact with GLU 69 (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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30A LEU 5.2 1.6 - - - +
31A SER* 5.1 13.9 - - - -
32A ASP 5.0 2.3 + - - +
65B VAL* 2.8 31.7 + - - +
66B ARG* 2.9 38.4 + - - +
68B ALA* 1.3 73.4 - - - +
70B LEU* 1.3 62.3 + - - +
72B ALA* 3.4 4.7 + - - +
73B ILE* 3.2 25.8 + - - +
83B PHE* 4.0 10.8 - - + -
99B SER* 2.8 30.4 + - - +
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Residues in contact with LEU 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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30A LEU* 4.4 8.3 - - + +
24B GLU* 4.8 0.2 - - - +
30B LEU* 6.3 0.7 - - + -
35B LEU* 3.7 22.0 - - + +
38B LEU* 4.0 19.1 - - + -
39B ILE* 3.6 25.2 - - + +
42B TYR* 3.6 37.2 - - + -
66B ARG* 2.9 47.3 + - - +
67B PHE* 3.8 3.6 - - - +
69B GLU* 1.3 73.0 - - - +
71B LYS* 1.3 66.5 + - - +
73B ILE* 3.2 13.2 + - + +
74B GLN* 3.1 22.3 + - - +
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Residues in contact with LYS 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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39B ILE* 3.7 27.2 - - + +
67B PHE* 2.9 43.6 + - + +
68B ALA 3.7 4.7 - - - +
70B LEU* 1.3 76.3 - - - +
72B ALA* 1.3 53.1 + - - +
74B GLN* 3.5 22.0 + - - +
75B GLU* 2.8 41.8 + - - +
78B ASP* 6.2 2.9 - - - -
79B ALA* 3.9 5.4 - - + -
82B TYR* 3.7 36.2 + - + -
88C ALA* 4.1 21.8 + - - +
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Residues in contact with ALA 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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32A ASP* 4.7 13.7 - - + +
68B ALA 2.9 16.6 + - - +
69B GLU* 3.5 7.6 - - - +
70B LEU 3.2 0.2 - - - -
71B LYS* 1.3 75.8 - - - +
73B ILE* 1.3 64.6 + - - +
76B PRO* 3.3 26.9 - - + +
79B ALA* 3.6 9.4 - - - +
83B PHE* 3.9 8.7 - - + -
103B PHE* 3.8 27.6 - - + -
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Residues in contact with ILE 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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30A LEU* 3.7 24.0 - - + +
31A SER* 3.7 20.2 - - - +
32A ASP* 3.5 30.1 - - - +
35A LEU* 3.7 16.4 - - + -
73A ILE* 3.6 35.6 - - + +
74A GLN* 5.2 3.3 - - - +
30B LEU* 5.4 4.3 - - + -
35B LEU* 3.9 10.8 - - + -
69B GLU 3.2 10.3 + - - +
70B LEU* 3.2 20.1 + - + +
72B ALA* 1.3 80.2 - - - +
74B GLN* 1.3 64.1 + - - +
76B PRO* 4.1 4.9 - - - +
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Residues in contact with GLN 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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73A ILE* 4.5 10.7 - - + +
76A PRO* 5.7 3.8 - - - +
32B ASP* 5.3 5.4 - - - +
35B LEU* 4.2 13.1 - - + +
36B ASN* 2.2 36.3 + - - +
39B ILE* 3.5 25.4 - - + +
70B LEU 3.1 13.0 + - - +
71B LYS* 3.5 26.8 + - - +
73B ILE* 1.3 84.7 - - - +
75B GLU* 1.3 66.4 + - + +
76B PRO* 4.2 1.0 - - - +
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Residues in contact with GLU 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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71B LYS* 2.8 23.5 + - - +
74B GLN* 1.3 81.2 - - + +
76B PRO* 1.3 72.6 - - - +
77B ASP* 3.0 37.9 + - - +
78B ASP* 3.1 36.6 + - + +
79B ALA 3.4 6.6 + - - -
123C ARG* 6.0 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
------------------------------------------------------------
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