Contacts of the helix formed by residues 68 - 73 (chain A) in PDB entry 4WNB
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 MET 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A MET* 3.6 19.7 - - + +
34A ILE* 3.9 11.2 - - - -
37A TRP* 3.5 44.0 - - + +
65A PRO* 2.9 38.2 + - + +
67A ALA* 1.3 75.6 - - - +
69A ILE* 1.3 66.2 + - - +
70A GLN 3.2 3.1 - - - -
71A VAL* 2.8 44.0 + - + +
72A TRP* 3.3 45.1 - - + +
26B ALA 4.9 0.7 - - - +
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PRO 4.3 0.6 + - - -
66A PRO 3.1 16.8 + - - +
67A ALA 3.3 0.8 - - - -
68A MET* 1.3 76.3 - - - +
70A GLN* 1.3 65.8 + - - +
71A VAL 3.3 0.2 + - - -
72A TRP* 3.4 21.4 + - + +
73A THR* 4.2 0.3 + - - -
109A GLN* 3.9 12.3 - - + +
111A TYR* 3.8 18.8 - - + -
115A LEU* 3.7 30.3 - - + -
121A VAL* 4.1 8.7 - - + -
150A TRP* 3.4 60.7 + - + -
157A VAL* 4.5 2.5 - - + -
158A ALA* 3.8 13.9 - - + -
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Residues in contact with GLN 70 (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 ALA 4.7 0.6 + - - -
68A MET 3.2 0.6 - - - -
69A ILE* 1.3 82.4 - - - +
71A VAL* 1.3 63.5 + - - +
72A TRP 3.3 0.7 + - - -
73A THR* 3.3 11.3 + - - +
74A MET* 3.3 31.4 + - - +
107A CYS* 4.9 2.8 - - - -
109A GLN* 3.1 23.3 + - - +
123A ILE* 6.0 1.6 - - + -
150A TRP* 3.7 22.7 - - + -
160A MET* 3.5 24.1 - - + +
53B LEU* 3.4 32.7 - - + +
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Residues in contact with VAL 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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33A MET* 4.1 6.3 - - + -
37A TRP* 4.1 11.7 - - + +
67A ALA 4.6 2.2 - - - +
68A MET* 2.8 43.2 + - + +
70A GLN* 1.3 78.4 - - - +
72A TRP* 1.3 61.0 + - - +
73A THR 3.2 0.7 + - - -
74A MET* 3.3 11.5 + - - +
26B ALA 3.8 12.1 - - - +
27B THR* 3.7 26.7 - - + +
28B ARG* 3.0 44.7 + - + -
53B LEU* 4.1 7.0 - - + -
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Residues in contact with TRP 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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25A ALA* 3.2 30.9 - - + +
26A ARG 3.7 4.5 + - - -
27A ASP* 4.7 6.9 + - + +
28A PRO 4.2 5.4 - - - -
29A VAL* 3.7 41.0 - - + +
30A ASN* 3.7 40.8 - - - -
33A MET* 3.5 31.2 - - + -
34A ILE* 4.0 3.6 - - + -
64A ALA* 4.0 10.1 - - + +
65A PRO 5.3 0.4 + - - -
68A MET* 3.3 58.8 + - + +
69A ILE* 3.4 25.0 - - + +
70A GLN 3.3 1.4 - - - -
71A VAL* 1.3 76.0 - - - +
73A THR* 1.3 59.2 + - + +
115A LEU* 4.6 3.8 - - + +
121A VAL* 4.5 7.9 - - + -
28B ARG* 3.2 13.4 + - - +
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Residues in contact with THR 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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23A ARG* 2.9 27.0 + - - +
25A ALA* 3.7 30.1 - - + +
26A ARG 5.3 0.4 - - - +
70A GLN* 3.3 8.3 + - - +
71A VAL 3.2 0.4 - - - -
72A TRP* 1.3 75.9 - - + +
74A MET* 1.3 66.9 + - - +
75A MET 3.4 0.2 + - - -
121A VAL* 4.2 11.2 - - + +
123A ILE* 3.7 35.0 - - + +
150A TRP* 3.0 33.5 + - + +
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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