Contacts of the strand formed by residues 73 - 77 (chain C) in PDB entry 4M75
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 VAL 73 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ILE* 3.9 12.6 - - + -
19C LYS 4.2 0.2 - - - -
20C LEU* 3.7 21.3 - - + -
37C SER* 3.9 28.3 - - - +
39C ILE* 4.6 5.8 - - + -
68C ILE* 4.0 13.7 - - + -
69C ARG 4.5 1.3 - - - +
70C GLY 3.0 11.1 + - - +
72C THR* 1.3 76.7 + - - +
74C THR* 1.3 63.1 + - - +
75C LEU* 4.0 9.9 - - - +
76C ILE* 4.2 25.4 - - + -
72D PHE* 5.6 0.9 - - + -
74D ARG* 3.2 24.1 - - + +
77D GLN* 3.8 7.7 - - - +
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Residues in contact with THR 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A VAL* 4.4 8.7 - - + +
19C LYS* 2.8 29.6 + - + +
20C LEU 3.9 1.2 - - - -
21C ARG* 3.6 30.7 + - - +
72C THR 3.4 0.2 + - - -
73C VAL* 1.3 74.6 - - - +
75C LEU* 1.3 73.0 + - + +
28D LEU* 3.6 28.9 - - + +
30D SER* 5.8 2.0 - - - +
32D LEU* 6.4 0.4 - - + -
34D TYR* 4.3 6.5 - - - +
73D LEU* 4.0 2.4 - - - +
74D ARG* 3.4 22.7 + - - +
77D GLN* 4.7 8.1 + - + +
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Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR* 3.7 7.1 - - + +
18C ILE* 3.4 4.9 - - - +
19C LYS* 2.9 76.8 + - + -
73C VAL* 3.9 1.1 - - - -
74C THR* 1.3 88.7 - - + +
76C ILE* 1.3 70.2 + - - +
77C SER* 5.3 1.6 - - - -
34D TYR* 4.0 11.4 - - + +
67D PHE* 3.9 24.9 - - + -
71D VAL* 3.5 25.8 - - + -
72D PHE* 3.1 14.8 - - - +
73D LEU* 3.2 13.0 - - + -
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Residues in contact with ILE 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 3.6 40.2 - - + -
11C ASN* 5.3 1.8 - - - +
16C VAL* 4.4 14.1 - - + -
17C TYR 3.2 7.6 - - - +
18C ILE* 4.2 10.3 - - + -
30C LEU* 6.1 0.9 - - + -
37C SER* 4.8 1.8 - - - +
39C ILE* 3.2 33.9 - - + -
73C VAL* 4.2 14.1 - - + -
75C LEU* 1.3 80.6 - - - +
77C SER* 1.3 72.9 + - - +
71D VAL* 3.6 1.4 - - - +
72D PHE* 2.7 51.7 + - + +
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Residues in contact with SER 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASN* 4.4 4.2 + - - +
16C VAL* 3.2 13.7 - - - +
17C TYR* 2.8 36.4 + - - -
75C LEU* 5.3 1.8 - - - -
76C ILE* 1.3 80.2 - - - +
78C THR* 1.3 91.4 + - - +
67D PHE* 4.3 19.0 - - - +
69D SER* 4.6 1.4 + - - -
70D ASP 3.4 19.7 + - - -
71D VAL* 4.5 9.9 - - - -
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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