Contacts of the strand formed by residues 76 - 81 (chain A) in PDB entry 1M6X
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 SER 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A PHE* 3.2 3.1 - - - +
71A ASP* 2.7 52.3 + - - +
74A ASN* 4.1 13.0 + - - +
75A LYS* 1.3 76.3 - - - +
77A LEU* 1.3 61.6 + - - +
100A TRP* 3.3 1.3 - - - -
101A GLU* 3.3 18.2 - - - -
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Residues in contact with LEU 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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19A PHE* 6.0 0.7 - - + -
23A PHE* 3.8 22.0 - - + -
31A ILE* 3.7 29.2 - - + -
34A CYS* 4.4 5.8 - - - -
38A LEU* 4.5 2.2 - - + -
68A LEU* 3.8 15.0 - - + -
69A SER 3.6 12.1 - - - +
70A PHE* 3.8 4.9 - - + +
76A SER* 1.3 75.0 - - - +
78A GLN* 1.3 65.6 + - - +
79A PHE* 3.5 32.8 - - + -
100A TRP* 4.0 10.3 - - + -
101A GLU 2.9 7.8 + - - +
102A PHE* 3.3 20.4 - - + -
103A THR* 3.2 21.1 + - - -
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Residues in contact with GLN 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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67A SER 3.8 2.8 + - - +
68A LEU* 3.6 2.6 - - - +
69A SER* 3.1 51.0 + - - +
77A LEU* 1.3 76.6 - - - +
79A PHE* 1.3 69.4 + - - +
103A THR* 3.1 32.7 - - - +
105A ILE* 3.4 24.5 - - + +
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Residues in contact with PHE 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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38A LEU* 3.2 41.1 - - + -
42A CYS* 3.5 22.7 - - - -
64A ILE* 3.8 21.5 - - + -
67A SER* 3.7 15.7 - - - +
68A LEU* 4.0 12.6 - - + +
77A LEU* 3.5 22.0 - - + -
78A GLN* 1.3 77.7 - - - +
80A LYS* 1.3 72.6 + - - +
81A TYR* 4.3 8.5 - - + -
93A LEU* 3.9 5.6 - - + -
102A PHE* 4.8 0.7 - + - -
103A THR 3.5 1.2 + - - -
104A ILE* 3.0 35.9 - - + -
105A ILE* 2.9 27.4 + - - +
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Residues in contact with LYS 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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63A ILE* 3.8 17.9 - - + +
64A ILE* 3.6 13.0 - - - +
67A SER* 2.8 30.6 + - - +
79A PHE* 1.3 82.5 - - - +
81A TYR* 1.3 64.4 + - - +
105A ILE* 3.1 34.3 - - + +
106A PRO 4.8 2.7 - - - +
107A TYR* 4.5 29.2 + - + -
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Residues in contact with TYR 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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39A THR* 4.7 4.9 - - + -
42A CYS* 3.6 29.7 + - + -
43A TRP* 3.5 38.8 - - - +
46A THR* 3.8 11.7 + - + -
47A HIS* 4.6 1.0 - - - -
60A TYR* 3.6 30.1 - + + -
63A ILE* 4.8 4.0 - - - -
64A ILE* 4.4 17.0 - - + -
79A PHE* 4.1 4.5 + - + -
80A LYS* 1.3 76.1 - - - +
82A LYS* 1.3 76.4 + - - +
83A THR* 2.7 42.0 + - + +
89A LEU* 4.2 8.1 - - + -
104A ILE* 3.8 16.8 - - + -
105A ILE 3.2 7.1 + - - +
106A PRO* 3.8 0.5 - - - +
107A TYR* 3.1 20.4 + - - +
21H G 4.9 2.6 + - - -
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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