Contacts of the helix formed by residues 70 - 85 (chain A) in PDB entry 4PCW
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 PHE 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ILE* 4.3 3.4 - - + -
11A ILE* 3.7 28.9 - - + -
14A PHE* 3.6 46.9 - + + -
25A ASP 4.2 2.2 + - - +
69A ASP* 1.3 75.8 - - - +
71A THR* 1.3 53.9 + - - +
73A PHE* 3.1 16.0 + + - +
74A LEU* 2.7 75.7 + - + +
81B ALA* 3.5 22.7 - - + -
82B GLN* 4.7 4.5 - - + -
85B TYR* 3.5 43.5 - + + -
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Residues in contact with THR 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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69A ASP* 3.2 10.9 + - - -
70A PHE* 1.3 79.5 - - - +
72A GLU* 1.3 64.5 + - + +
74A LEU* 3.1 9.7 + - - +
75A LEU* 3.0 25.9 + - + +
78B PHE* 3.9 7.1 - - + -
82B GLN* 3.1 32.1 + - - +
62C ILE* 3.7 36.8 + - + +
63C ASP* 5.5 1.9 - - + +
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Residues in contact with GLU 72 (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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60A LEU* 3.4 27.8 - - - +
61A ASP* 4.1 0.6 - - - +
62A ILE* 3.0 34.9 + - + +
63A ASP* 3.2 11.8 + - - +
67A LYS 3.1 8.7 - - - +
68A ILE* 3.4 10.1 - - + +
69A ASP* 2.9 35.6 + - - +
71A THR* 1.3 74.1 - - + +
73A PHE* 1.3 62.4 + - - +
75A LEU* 3.6 17.3 + - + +
76A MET* 3.6 10.9 + - - +
101A CA 2.5 30.7 - - - -
103A 2PE 5.1 1.4 - - - +
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Residues in contact with PHE 73 (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 ILE* 3.8 19.3 - - + -
13A LEU* 3.8 22.4 - - + -
14A PHE* 3.6 36.6 - + + -
27A LEU* 4.3 8.7 - - + -
32A LEU* 5.8 1.1 - - + -
35A LEU* 4.2 24.2 - - + -
60A LEU* 4.9 2.7 - - + -
68A ILE* 3.9 9.7 - - + +
69A ASP 3.0 13.5 + - - +
70A PHE* 3.3 17.7 - + - +
72A GLU* 1.3 76.7 - - - +
74A LEU* 1.3 65.5 + - + +
76A MET* 3.1 26.4 + - + +
77A VAL* 3.1 43.7 + - + +
3B LEU* 4.3 8.1 - - + -
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Residues in contact with LEU 74 (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 ILE* 4.2 16.2 - - + -
70A PHE* 2.7 62.9 + - + +
71A THR* 3.4 8.1 - - - +
73A PHE* 1.3 74.9 - - + +
75A LEU* 1.3 63.3 + - - +
77A VAL* 3.0 6.5 + - + +
78A PHE* 2.9 51.1 + - + -
78B PHE* 3.9 15.7 - - + -
81B ALA* 3.6 20.9 - - + -
82B GLN* 3.9 20.2 - - + -
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Residues in contact with LEU 75 (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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60A LEU 6.1 0.2 - - - +
62A ILE* 3.8 28.5 - - + -
71A THR* 3.0 19.8 + - + +
72A GLU* 3.7 12.1 - - - +
73A PHE 3.3 0.2 - - - -
74A LEU* 1.3 75.3 - - - +
76A MET* 1.3 58.3 + - - +
78A PHE* 3.7 4.5 + - - +
79A LYS* 3.1 31.7 + - - +
103A 2PE 4.1 28.7 - - - +
78B PHE* 4.1 10.1 - - + -
62C ILE* 4.6 7.6 - - + -
75C LEU* 4.2 21.5 - - + -
103C 2PE 4.0 36.3 - - - +
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Residues in contact with MET 76 (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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32A LEU* 5.1 1.8 - - + -
36A LEU* 4.7 3.1 - - + -
40A PHE* 3.8 24.7 - - + -
44A LEU* 4.4 4.5 - - - -
56A PHE* 3.9 16.4 - - + -
60A LEU* 3.7 39.9 - - + -
72A GLU 3.6 1.4 + - - +
73A PHE* 3.1 21.6 + - + +
74A LEU 3.1 0.6 - - - -
75A LEU* 1.3 77.6 - - - +
77A VAL* 1.3 69.3 + - - +
79A LYS* 3.2 6.9 + - - +
80A LEU* 3.0 41.8 + - - +
103A 2PE 3.9 32.0 + - - +
3B LEU* 5.7 0.2 - - - -
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Residues in contact with VAL 77 (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 ILE* 4.3 22.4 - - + -
73A PHE* 3.1 49.0 + - + +
74A LEU* 3.0 11.1 + - + +
76A MET* 1.3 82.1 - - - +
78A PHE* 1.3 69.8 + - + +
80A LEU* 3.3 6.1 + - - +
81A ALA* 3.0 25.1 + - + +
3B LEU* 4.1 13.2 - - + -
7B ILE* 3.9 27.1 - - + +
10B ILE* 6.1 0.9 - - + -
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Residues in contact with PHE 78 (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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7A ILE* 6.2 0.2 - - + -
10A ILE* 5.4 4.5 - - + -
74A LEU* 2.9 52.5 + - + +
75A LEU* 4.3 2.7 - - - +
77A VAL* 1.3 82.5 - - + +
79A LYS* 1.3 60.8 + - - +
81A ALA* 3.8 6.5 - - + -
82A GLN* 2.9 28.1 + - - +
10B ILE* 4.8 9.4 - - + -
74B LEU* 3.5 30.0 - - + +
77B VAL* 3.5 31.0 - - + -
78B PHE* 3.6 44.6 - + + -
81B ALA* 4.7 2.7 - - + -
103C 2PE 4.0 23.4 + - - +
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Residues in contact with LYS 79 (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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75A LEU 3.1 20.2 + - - +
76A MET* 3.2 7.2 + - - +
78A PHE* 1.3 76.3 - - - +
80A LEU* 1.3 60.0 + - - +
82A GLN* 3.4 12.2 + - - +
83A ALA* 2.8 29.7 + - - +
103A 2PE 3.2 116.7 + - - +
103C 2PE 5.8 2.7 - - - +
71D THR* 4.5 17.7 + - + +
75D LEU* 4.2 9.5 - - - +
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Residues in contact with LEU 80 (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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40A PHE* 5.1 7.0 - - + -
43A ILE* 6.1 0.9 - - + -
44A LEU* 4.1 18.6 - - + -
76A MET* 3.0 35.6 + - - +
77A VAL* 3.5 8.1 - - - +
79A LYS* 1.3 75.2 - - - +
81A ALA* 1.3 55.8 + - - +
83A ALA* 3.0 3.5 + - - +
84A TYR* 2.6 61.8 + - + +
103A 2PE 3.1 54.3 - - - +
3B LEU* 5.3 3.8 - - + -
4B LEU* 5.6 2.9 - - + -
7B ILE* 4.2 17.5 - - + -
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Residues in contact with ALA 81 (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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77A VAL* 3.0 15.2 + - + +
78A PHE* 3.8 13.0 - - + +
80A LEU* 1.3 76.2 - - - +
82A GLN* 1.3 62.6 + - - +
84A TYR 3.3 0.2 + - - -
85A TYR* 3.0 25.5 + - - +
7B ILE* 3.5 28.8 - - + +
10B ILE* 5.8 3.1 - - + -
11B ILE* 3.5 9.1 - - + +
70B PHE* 3.6 10.0 - - + -
74B LEU* 4.2 15.0 - - + -
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Residues in contact with GLN 82 (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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78A PHE 2.9 18.1 + - - +
79A LYS* 3.6 12.1 - - - +
80A LEU 3.2 0.2 - - - -
81A ALA* 1.3 75.9 - - - +
83A ALA* 1.3 60.8 + - - +
85A TYR* 3.6 13.7 - - - +
86A GLU 4.7 0.5 + - - -
103A 2PE 4.8 6.2 - - - -
70B PHE* 4.0 13.7 - - + -
71B THR* 3.3 28.1 + - - +
74B LEU* 4.1 6.7 - - + +
82C GLN* 2.9 37.7 + - - +
103C 2PE 3.1 21.3 + - - -
71D THR* 6.1 1.3 - - - -
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Residues in contact with ALA 83 (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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79A LYS 2.8 17.6 + - - +
80A LEU 3.0 4.0 + - - +
82A GLN* 1.3 75.0 - - - +
84A TYR* 1.3 60.0 + - - +
85A TYR 3.1 2.1 + - - -
86A GLU* 2.9 26.9 + - - +
103A 2PE 3.9 30.7 - - - -
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Residues in contact with TYR 84 (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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43A ILE* 3.1 30.0 - - - +
80A LEU* 2.6 55.0 + - + +
83A ALA* 1.3 68.6 - - - +
85A TYR* 1.3 53.4 + - - +
86A GLU* 2.8 36.0 + - - +
87A SER 4.4 4.7 - - - -
103A 2PE 3.4 31.3 + - - -
4B LEU* 3.6 25.9 - - + +
7B ILE* 4.7 4.3 - - + -
8B PHE* 3.6 34.2 - + + -
11B ILE* 3.7 19.7 - - + +
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Residues in contact with TYR 85 (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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81A ALA 3.0 17.5 + - - +
82A GLN 3.6 11.9 - - - +
83A ALA 3.1 0.6 - - - -
84A TYR* 1.3 75.6 - - - +
86A GLU* 1.3 51.9 + - - +
87A SER* 2.6 22.1 + - - -
11B ILE* 3.9 24.0 - - + +
14B PHE* 3.5 36.4 - + - -
15B LYS* 4.3 21.8 - - + +
24B THR 4.5 1.7 + - - -
25B ASP* 3.6 32.6 + - + +
70B PHE* 3.8 33.2 - + + -
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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
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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