Contacts of the strand formed by residues 76 - 81 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70D PHE* 3.2 3.6 - - - +
71D ASP* 2.8 51.7 + - - +
74D ASN* 4.1 12.7 + - - +
75D LYS* 1.3 76.3 - - - +
77D LEU* 1.3 60.1 + - - +
100D TRP* 3.2 1.7 - - - -
101D GLU* 3.4 18.2 - - - -
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PHE* 6.0 0.2 - - + -
23D PHE* 3.8 21.8 - - + -
31D ILE* 3.7 29.4 - - + -
34D CYS* 4.5 6.7 - - - -
38D LEU* 4.5 2.2 - - + -
68D LEU* 3.8 14.8 - - + -
69D SER 3.5 12.3 - - - +
70D PHE* 3.8 4.7 - - + -
76D SER* 1.3 75.2 - - - +
78D GLN* 1.3 63.3 + - - +
79D PHE* 3.5 32.7 - - + -
100D TRP* 4.0 9.6 - - + -
101D GLU 2.9 7.8 + - - +
102D PHE* 3.3 19.6 - - + +
103D THR* 3.2 20.9 + - - -
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Residues in contact with GLN 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D SER 3.9 3.0 + - - +
68D LEU* 3.5 2.3 - - - +
69D SER* 3.1 51.7 + - - +
77D LEU* 1.3 75.3 - - - +
79D PHE* 1.3 70.4 + - - +
103D THR* 3.1 32.7 - - - +
105D ILE* 3.4 24.9 - - + +
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Residues in contact with PHE 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LEU* 3.2 44.6 - - + -
42D CYS* 3.6 20.4 - - - -
64D ILE* 3.8 21.1 - - + -
67D SER* 3.7 16.8 - - - +
68D LEU* 4.0 12.6 - - + +
77D LEU* 3.5 22.0 - - + -
78D GLN* 1.3 78.3 - - - +
80D LYS* 1.3 71.6 + - - +
81D TYR* 4.2 8.7 - - + -
93D LEU* 3.9 5.2 - - + -
102D PHE* 4.8 1.1 - + - -
103D THR 3.5 1.4 + - - -
104D ILE* 3.0 35.2 - - + -
105D ILE* 2.9 26.7 + - - -
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Residues in contact with LYS 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ILE* 3.8 17.7 - - + +
64D ILE* 3.7 12.8 - - - +
67D SER* 2.7 31.4 + - - +
79D PHE* 1.3 81.7 - - - +
81D TYR* 1.3 65.5 + - - +
105D ILE* 3.1 33.0 - - + +
106D PRO 5.2 2.0 - - - -
107D TYR* 4.5 29.8 + - + -
114D SER* 4.8 11.7 + - - -
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Residues in contact with TYR 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D THR* 4.7 5.8 - - - -
42D CYS* 3.6 28.7 + - + -
43D TRP* 3.6 37.1 - - - +
46D THR* 3.9 11.5 + - + -
47D HIS* 4.6 1.4 - + - -
60D TYR* 3.6 30.1 - + + -
63D ILE* 4.8 4.3 - - - -
64D ILE* 4.4 18.4 - - + -
79D PHE* 4.1 5.8 + - + -
80D LYS* 1.3 77.0 - - - +
82D LYS* 1.3 83.8 + - - +
83D THR* 2.7 35.7 + - + +
89D LEU* 4.3 7.9 - - + -
104D ILE* 3.8 16.8 - - + -
105D ILE 3.1 7.7 + - - +
106D PRO* 3.8 0.5 - - - +
107D TYR* 3.1 21.0 + - - +
21J G 5.2 1.3 - - - -
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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
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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