Contacts of the helix formed by residues 71 - 82 (chain A) in PDB entry 5W5T
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 ALA 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ALA* 5.0 1.8 - - - -
67A THR* 3.6 32.8 - - + +
68A GLN 3.9 13.4 + - - +
69A TYR 3.1 3.6 + - - +
70A LYS* 1.3 75.9 - - - +
72A HIS* 1.3 65.3 + - - +
73A SER 3.5 0.9 - - - -
74A LEU* 3.2 10.1 + - + +
75A ILE* 2.9 33.9 + - + +
97A PRO* 5.7 0.9 - - + -
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Residues in contact with HIS 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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33A ARG 6.2 0.2 - - - +
70A LYS 3.4 3.7 + - - -
71A ALA* 1.3 78.6 - - - +
73A SER* 1.3 73.1 + - - +
75A ILE* 3.2 6.2 + - - +
76A ARG* 3.0 49.1 + - + +
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Residues in contact with SER 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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33A ARG 4.4 4.6 + - - -
34A ARG* 3.8 27.4 + - - +
38A ALA* 4.2 5.9 - - - +
46A ARG* 4.4 15.9 + - - -
70A LYS 4.8 1.2 + - - -
71A ALA 3.5 0.2 - - - -
72A HIS* 1.3 89.9 - - - +
74A LEU* 1.3 61.3 + - - +
76A ARG* 3.8 9.5 - - - +
77A HIS* 2.9 29.6 + - - +
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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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20A ALA* 3.6 30.3 - - + +
35A ALA* 4.2 12.3 - - + -
37A PRO* 4.2 7.4 - - + -
38A ALA* 3.8 29.1 - - + +
48A ILE* 3.9 34.1 - - + -
67A THR* 3.9 23.8 - - + -
70A LYS 5.2 1.1 + - - +
71A ALA* 3.2 12.3 + - - +
72A HIS 3.2 0.2 - - - -
73A SER* 1.3 81.3 + - - +
75A ILE* 1.3 56.5 + - - +
77A HIS* 3.4 7.5 + - + +
78A LEU* 3.0 37.5 + - + +
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Residues in contact with ILE 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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67A THR* 3.9 11.2 - - + +
71A ALA* 2.9 40.8 + - + +
72A HIS* 3.6 6.3 - - - +
74A LEU* 1.3 74.6 - - - +
76A ARG* 1.3 59.4 + - - +
78A LEU* 3.2 8.6 + - - +
79A GLN* 3.0 49.2 + - - +
95A ILE* 4.0 22.2 - - + -
97A PRO* 3.8 29.6 - - + -
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Residues in contact with ARG 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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72A HIS* 3.0 40.9 + - + +
73A SER* 3.8 7.9 - - - +
74A LEU 3.3 0.2 - - - -
75A ILE* 1.3 74.8 - - - +
77A HIS* 1.3 65.8 + - - +
79A GLN* 3.3 15.6 + - - +
80A ARG* 3.0 70.4 + - + +
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Residues in contact with HIS 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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46A ARG* 3.2 44.1 + - + +
48A ILE* 4.3 14.1 - - + -
49A ASP* 2.9 30.2 + - - -
73A SER 2.9 18.3 + - - +
74A LEU* 3.5 7.4 - - + +
76A ARG* 1.3 76.9 - - - +
78A LEU* 1.3 63.6 + - + +
80A ARG* 3.9 4.2 - - - +
81A GLY* 2.8 29.3 + - - -
82A TRP* 4.3 5.2 + + - -
302A THR* 3.5 21.3 - - - -
303A TYR* 3.7 27.6 - - + +
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Residues in contact with LEU 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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48A ILE* 4.5 8.7 - - + -
52A LEU* 3.7 30.7 - - + -
65A VAL* 3.8 30.5 - - + -
67A THR* 4.9 1.6 - - + -
74A LEU* 3.0 28.4 + - + +
75A ILE* 3.2 8.9 + - - +
77A HIS* 1.3 82.8 - - + +
79A GLN* 1.3 58.8 + - - +
82A TRP* 2.9 41.2 + - + +
93A PHE* 3.9 12.7 - - + -
95A ILE* 3.6 33.0 - - + +
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Residues in contact with GLN 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 ILE* 3.0 35.7 + - - +
76A ARG* 3.7 17.6 - - - +
77A HIS 3.3 0.2 - - - -
78A LEU* 1.3 75.6 - - - +
80A ARG* 1.3 64.1 + - + +
83A ASP* 3.4 20.1 - - - +
95A ILE* 4.0 14.2 - - + +
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Residues in contact with ARG 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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76A ARG* 3.0 67.7 + - + +
77A HIS* 3.9 2.9 - - - +
79A GLN* 1.3 80.7 - - + +
81A GLY* 1.3 58.9 + - - +
83A ASP* 3.3 19.4 - - - +
303A TYR* 3.7 55.7 + - + -
305A GLU* 3.9 7.9 + - - -
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Residues in contact with GLY 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 HIS 2.8 15.4 + - - -
80A ARG* 1.3 79.6 - - - +
82A TRP* 1.3 65.9 + - - +
83A ASP* 3.4 9.3 + - - +
84A PHE* 3.9 1.0 - - - -
301A TRP* 2.9 26.7 + - - -
303A TYR* 3.8 26.0 - - - -
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Residues in contact with TRP 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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49A ASP* 3.0 24.7 + - - -
52A LEU* 3.4 57.2 - - + +
53A SER* 3.7 11.4 - - - -
56A LEU* 4.4 7.4 - - + -
63A ILE* 4.8 0.9 - - + -
77A HIS* 4.3 5.3 + - - -
78A LEU* 2.9 29.8 + - + +
81A GLY* 1.3 81.4 - - - +
83A ASP* 1.3 57.7 + - - +
84A PHE* 3.5 25.0 + + - -
85A PHE* 3.8 27.8 - + - -
93A PHE* 3.6 46.2 - + + +
301A TRP* 3.4 38.7 + + + -
302A THR* 4.6 2.0 - - - +
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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