Contacts of the helix formed by residues 70 - 80 (chain B) in PDB entry 4XX1
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 LEU 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B ASN* 3.4 39.7 + - + +
48B TRP* 4.0 26.0 - - + +
49B MET* 3.7 12.6 - - - -
68B LEU 3.2 1.8 + - - -
69B PRO* 1.3 77.1 - - + +
71B GLY* 1.3 59.9 + - - +
72B VAL 3.4 2.2 - - - +
73B ASP* 3.9 17.8 - - - +
74B CYS* 3.0 29.7 + - - -
92G SER* 3.5 19.7 - - - +
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Residues in contact with GLY 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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49B MET* 4.3 12.3 - - - -
66B MET* 3.3 21.7 - - - +
68B LEU* 3.2 3.9 + - - -
69B PRO 3.0 9.4 + - - -
70B LEU* 1.3 77.1 - - - +
72B VAL* 1.3 65.0 + - - +
74B CYS* 3.3 7.1 + - - +
75B TRP* 3.2 19.4 + - - +
106E PHE* 3.9 6.4 - - - -
107E TYR* 4.9 7.6 - - - -
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Residues in contact with VAL 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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66B MET* 4.1 9.2 - - - +
67B PHE* 3.9 31.4 - - + -
68B LEU 3.9 7.8 + - - +
70B LEU 3.4 0.4 - - - +
71B GLY* 1.3 76.2 - - - +
73B ASP* 1.3 63.8 + - - +
75B TRP* 3.1 8.6 + - + +
76B ILE* 2.9 37.3 + - + +
241B GLU* 5.5 4.5 - - + -
242B GLU 5.3 6.1 - - - +
244B ARG* 4.8 13.9 - - + +
245B ILE* 4.2 24.2 - - + -
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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
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46B VAL* 4.9 10.8 - - + +
47B ASN* 4.0 14.0 + - - +
70B LEU* 3.7 22.1 + - - +
71B GLY 3.2 0.2 - - - -
72B VAL* 1.3 85.0 - - - +
74B CYS* 1.3 60.4 + - - +
76B ILE* 3.5 10.7 + - - +
77B ASP* 3.4 20.4 + - - +
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Residues in contact with CYS 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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46B VAL* 5.7 0.2 - - - -
47B ASN* 3.2 11.9 - - - -
49B MET* 4.2 5.2 - - - -
50B CYS* 2.0 55.9 - - + -
70B LEU 3.0 22.4 + - - -
71B GLY 3.6 7.6 - - - +
72B VAL 3.2 0.4 - - - -
73B ASP* 1.3 73.6 - - - +
75B TRP* 1.3 60.1 + - - +
77B ASP* 3.4 8.7 + - - +
78B ASN* 2.5 32.2 + - - +
106E PHE* 4.1 14.6 - - + -
107E TYR* 4.5 5.2 - - + -
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Residues in contact with TRP 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.7 4.5 - - + -
60B ILE* 2.8 38.4 + - + -
61B TRP* 3.6 25.7 - + + +
66B MET* 3.5 28.0 - - + +
71B GLY 3.2 9.6 + - - +
72B VAL 3.3 9.6 - - - +
74B CYS* 1.3 76.6 - - - +
76B ILE* 1.3 84.3 + - + +
78B ASN* 2.9 15.8 + - - +
79B THR* 3.0 51.0 + - + +
146B TRP* 4.5 11.4 - + - -
245B ILE* 3.5 30.5 - - + -
247B THR* 3.7 22.7 - - - -
106E PHE* 3.8 16.1 - + + -
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Residues in contact with ILE 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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72B VAL* 2.9 27.1 + - + +
73B ASP* 3.6 13.2 - - - +
74B CYS 3.3 0.2 - - - -
75B TRP* 1.3 99.7 - - + +
77B ASP* 1.3 60.8 + - + +
78B ASN 3.0 5.2 + - - -
79B THR* 3.7 1.8 + - - -
80B ARG* 3.1 32.7 + - + +
244B ARG 6.0 0.2 - - - +
245B ILE* 5.4 0.2 - - + -
246B THR* 3.7 29.8 - - + +
247B THR* 4.2 9.6 - - + -
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Residues in contact with ASP 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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42B LYS* 3.4 28.9 - - - +
44B ASP* 5.1 7.7 - - - +
45B VAL* 5.5 0.2 - - - -
46B VAL* 3.4 35.1 + - + +
50B CYS* 6.1 0.4 - - - -
73B ASP 3.4 9.2 + - - +
74B CYS* 3.4 4.9 + - - +
75B TRP 3.2 0.8 - - - -
76B ILE* 1.3 79.2 - - + +
78B ASN* 1.3 60.8 + - - +
80B ARG* 3.2 35.7 + - - +
93B ALA* 3.7 11.1 - - - +
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Residues in contact with ASN 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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40B LEU* 3.5 25.4 - - + +
42B LYS* 2.6 34.3 + - - +
50B CYS* 5.6 2.4 - - - +
60B ILE* 4.5 18.4 - - + -
74B CYS* 2.5 30.5 + - - +
75B TRP* 2.9 7.5 + - - +
77B ASP* 1.3 79.7 - - - +
79B THR* 1.3 63.3 + - - +
80B ARG* 3.0 11.1 + - - +
93B ALA* 4.2 7.5 + - - +
96B VAL* 4.0 14.8 - - + +
98B ILE* 4.0 16.6 - - + +
147B ARG* 4.1 0.2 + - - -
106E PHE* 4.6 11.6 - - - +
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Residues in contact with THR 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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36B LEU* 6.5 0.9 - - + -
60B ILE* 4.6 8.5 - - + -
75B TRP* 3.0 70.0 + - + +
76B ILE* 3.7 4.3 + - - -
78B ASN* 1.3 74.4 - - + +
80B ARG* 1.3 70.7 + - - +
81B VAL* 3.5 2.3 + - - +
98B ILE* 4.8 3.4 - - + -
146B TRP* 5.8 1.8 - - + -
147B ARG* 2.9 37.9 + - - +
247B THR* 4.3 9.9 - - - +
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Residues in contact with ARG 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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42B LYS* 6.2 0.4 - - - +
44B ASP* 5.7 3.4 + - - -
76B ILE* 3.1 25.2 + - + +
77B ASP* 3.2 37.5 + - - +
78B ASN 3.0 5.9 - - - +
79B THR* 1.3 82.3 + - - +
81B VAL* 1.3 70.9 + - - +
82B VAL* 3.5 23.8 - - + +
92B ASN* 4.3 0.2 - - - -
93B ALA* 3.7 24.0 + - + +
94B PRO* 3.5 28.3 - - - +
147B ARG* 3.5 8.3 + - - -
247B THR* 6.4 0.9 - - - -
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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