Contacts of the helix formed by residues 69 - 88 (chain B) 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 ASP 69 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B PHE* 3.8 2.2 - - - -
25B ASP 4.0 4.5 - - - +
26B THR* 4.0 20.1 - - + +
63B ASP* 4.0 10.9 - - - +
65B ASN* 5.5 1.2 + - - -
67B LYS 3.9 1.2 + - - -
68B ILE* 1.3 75.3 - - - +
70B PHE* 1.3 58.4 + - - +
71B THR* 3.3 9.3 + - - -
72B GLU* 2.7 55.4 + - - +
73B PHE* 2.9 25.8 + - - +
102B CA 4.1 0.9 - - - -
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Residues in contact with PHE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA* 3.6 23.3 - - + -
82A GLN* 4.3 8.3 - - + -
85A TYR* 3.8 36.3 - + + -
10B ILE* 4.2 1.8 - - + -
11B ILE* 3.6 31.9 - - + -
14B PHE* 3.5 52.5 - + + -
25B ASP 4.4 1.6 + - - -
69B ASP* 1.3 75.2 - - - +
71B THR* 1.3 53.6 + - - +
73B PHE* 3.1 14.2 + + - +
74B LEU* 2.7 69.0 + - + +
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLN* 3.3 32.1 + - - +
69B ASP* 3.3 7.9 + - - +
70B PHE* 1.3 77.9 - - - +
72B GLU* 1.3 62.8 + - + +
74B LEU* 3.3 11.4 + - - +
75B LEU* 3.2 20.1 + - - +
79C LYS* 4.5 24.5 + - + -
82C GLN* 5.1 1.6 - - - +
103C 2PE 4.2 14.9 - - - +
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Residues in contact with GLU 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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60B LEU* 3.3 32.0 - - - +
61B ASP* 4.1 0.9 - - - -
62B ILE* 2.8 33.9 + - + +
63B ASP* 3.4 8.4 + - - +
67B LYS 3.1 4.1 - - - +
68B ILE* 3.3 9.0 - - + -
69B ASP* 2.7 50.3 + - - +
71B THR* 1.3 73.2 - - - +
73B PHE* 1.3 62.0 + - - +
75B LEU* 3.3 19.8 - - - +
76B MET 3.7 2.8 + - - -
102B CA 2.5 30.1 - - - -
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Residues in contact with PHE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 4.5 3.4 - - + -
10B ILE* 3.7 26.0 - - + -
13B LEU* 3.4 30.1 - - + -
14B PHE* 3.7 28.5 - + + -
27B LEU* 4.3 8.5 - - + -
32B LEU* 6.0 2.9 - - + -
35B LEU* 4.1 15.0 - - + -
60B LEU* 5.6 2.2 - - + -
68B ILE* 3.7 10.5 - - + +
69B ASP 2.9 14.1 + - - +
70B PHE* 3.3 17.5 - + - +
72B GLU* 1.3 73.1 - - - +
74B LEU* 1.3 61.7 + - + +
75B LEU 3.0 2.0 - - - -
76B MET* 2.9 50.6 + - + +
77B VAL* 3.2 27.4 + - + +
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Residues in contact with LEU 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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78A PHE* 3.5 48.3 - - + +
81A ALA* 4.2 4.7 - - + -
82A GLN* 4.1 7.2 - - + +
10B ILE* 4.2 13.5 - - + -
70B PHE* 2.7 61.0 + - + +
71B THR* 3.3 9.4 + - - +
73B PHE* 1.3 82.2 - - + +
75B LEU* 1.3 52.4 + - - +
77B VAL* 3.2 5.5 + - + +
78B PHE* 2.8 34.8 + - - +
103C 2PE 4.0 19.4 - - - +
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Residues in contact with LEU 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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59B HIS 4.9 1.1 - - - +
60B LEU* 4.9 8.3 - - + +
62B ILE* 5.0 5.8 - - + -
71B THR 3.2 11.0 + - - +
72B GLU* 3.3 15.7 - - - +
73B PHE 3.0 0.6 - - - -
74B LEU* 1.3 78.0 - - - +
76B MET* 1.3 60.8 + - - +
78B PHE* 3.3 9.7 + - + +
79B LYS* 3.0 37.5 + - - +
59C HIS* 3.3 47.8 - - + +
79C LYS* 4.2 10.5 - - - +
103C 2PE 4.1 40.6 - - - +
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Residues in contact with MET 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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3A LEU* 3.5 32.3 - - + -
32B LEU* 5.9 1.8 - - - -
35B LEU* 5.0 2.2 - - + -
36B LEU* 4.1 8.1 - - - -
40B PHE* 3.8 20.0 - - + -
56B PHE* 3.9 30.5 - - + -
60B LEU* 3.9 27.2 - - + +
72B GLU 3.7 1.2 + - - -
73B PHE* 2.9 33.6 + - + +
75B LEU* 1.3 78.0 - - - +
77B VAL* 1.3 69.8 + - + +
79B LYS* 3.2 11.3 + - - +
80B LEU* 3.0 30.0 + - + +
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Residues in contact with VAL 77 (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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3A LEU* 4.2 7.9 - - + -
7A ILE* 4.0 23.6 - - + +
10A ILE* 6.0 0.2 - - + -
78A PHE* 3.5 24.0 - - + -
10B ILE* 4.2 16.8 - - + -
73B PHE* 3.2 44.8 + - + +
74B LEU* 3.2 7.8 + - - +
76B MET* 1.3 85.9 - - + +
78B PHE* 1.3 62.9 + - - +
80B LEU* 3.4 7.1 + - - +
81B ALA* 3.1 22.0 + - - +
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Residues in contact with PHE 78 (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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71A THR* 3.9 13.0 - - + -
74A LEU* 3.9 23.6 - - + -
75A LEU* 4.1 16.2 - - + -
78A PHE* 3.6 31.4 - + + -
74B LEU 2.8 18.1 + - - +
75B LEU* 3.5 13.2 - - + +
77B VAL* 1.3 77.2 - - - +
79B LYS* 1.3 67.3 + - + +
81B ALA* 3.3 4.0 + - - +
82B GLN* 3.2 58.9 + - - +
59C HIS 5.6 0.2 - - - -
62C ILE* 3.8 24.2 - - + -
103C 2PE 3.7 27.1 - - - -
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Residues in contact with LYS 79 (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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59B HIS* 6.1 1.1 - - - -
60B LEU* 5.8 3.1 - - + -
75B LEU* 3.0 33.6 + - + +
76B MET* 3.5 10.8 - - - +
78B PHE* 1.3 82.3 - - + +
80B LEU* 1.3 62.6 + - - +
82B GLN* 3.3 10.6 + - - +
83B ALA* 3.0 23.8 + - - +
58C ASP* 3.4 35.6 + - - +
59C HIS* 3.2 44.4 + - - +
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Residues in contact with LEU 80 (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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3A LEU* 4.6 0.4 - - + -
4A LEU* 5.0 1.6 - - + -
7A ILE* 3.6 25.4 - - + -
40B PHE* 3.3 43.1 - - + -
76B MET* 3.0 25.8 + - + +
77B VAL* 3.7 4.3 - - - +
79B LYS* 1.3 75.6 - - - +
81B ALA* 1.3 63.9 + - - +
83B ALA* 3.3 6.1 + - + +
84B TYR* 3.0 56.5 + - + +
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Residues in contact with ALA 81 (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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7A ILE* 3.7 22.8 - - + +
10A ILE* 5.9 2.5 - - + -
11A ILE* 3.9 2.9 - - + +
70A PHE* 3.5 10.7 - - + -
74A LEU* 3.6 27.4 - - + -
78A PHE* 4.7 3.8 - - + -
77B VAL 3.1 16.6 + - - +
78B PHE* 3.6 6.5 - - - +
79B LYS 3.3 0.2 - - - -
80B LEU* 1.3 77.3 - - - +
82B GLN* 1.3 61.1 + - - +
84B TYR 3.6 0.9 + - - -
85B TYR* 3.0 24.8 + - - +
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Residues in contact with GLN 82 (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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70A PHE* 4.6 4.9 - - + -
71A THR* 3.1 20.4 + - - +
74A LEU* 3.9 13.9 - - + -
78B PHE* 3.2 43.7 + - + +
79B LYS* 3.6 12.0 - - - +
80B LEU 3.3 0.2 - - - -
81B ALA* 1.3 80.2 - - - +
83B ALA* 1.3 62.6 + - - +
85B TYR* 3.3 18.5 + - - +
86B GLU* 3.6 12.6 + - - +
62C ILE* 2.9 27.0 + - - +
64C HIS* 3.4 25.7 + - + -
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Residues in contact with ALA 83 (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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79B LYS 3.0 17.0 + - - +
80B LEU* 3.7 9.6 - - + +
82B GLN* 1.3 75.9 - - - +
84B TYR* 1.3 62.3 + - + +
85B TYR 3.1 0.2 - - - -
86B GLU* 3.0 28.6 + - - +
87B SER* 3.5 8.2 + - - -
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Residues in contact with TYR 84 (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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4A LEU* 3.9 25.9 - - + +
7A ILE* 4.9 4.5 - - + -
8A PHE* 3.7 28.0 - + + -
11A ILE* 3.8 20.1 - - + +
80B LEU* 3.0 50.0 + - + +
83B ALA* 1.3 75.8 - - + +
85B TYR* 1.3 61.4 + - - +
86B GLU 3.1 1.6 - - - -
87B SER* 3.6 21.5 - - - -
88B THR* 3.0 27.5 + - - +
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Residues in contact with TYR 85 (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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11A ILE* 4.0 17.0 - - + -
14A PHE* 3.6 22.0 - + - -
15A LYS* 4.1 23.1 + - + +
24A THR 4.3 1.7 + - - -
25A ASP* 3.5 43.0 + - + -
70A PHE* 3.5 45.1 - + + -
81B ALA 3.0 18.4 + - - +
82B GLN 3.4 7.6 - - - +
83B ALA 3.1 0.4 - - - -
84B TYR* 1.3 78.2 - - - +
86B GLU* 1.3 72.4 + - - +
88B THR* 2.9 21.5 - - - +
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Residues in contact with GLU 86 (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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82B GLN 3.7 14.4 - - - +
83B ALA* 3.0 10.2 + - - +
85B TYR* 1.3 92.7 - - - +
87B SER* 1.3 64.6 + - - +
88B THR* 4.2 2.3 + - - -
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Residues in contact with SER 87 (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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83B ALA 3.5 10.3 + - - -
84B TYR* 3.4 28.5 + - - -
86B GLU* 1.3 79.0 - - - +
88B THR* 1.3 77.6 + - - +
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Residues in contact with THR 88 (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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8A PHE* 5.8 6.2 - - - -
11A ILE* 4.6 6.3 - - + -
15A LYS* 3.3 34.4 + - + +
84B TYR* 3.0 11.2 + - - +
85B TYR* 2.9 32.5 - - - +
86B GLU 4.2 2.6 + - - -
87B SER* 1.3 92.3 + - - +
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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
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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