Contacts of the strand formed by residues 51 - 58 (chain C) in PDB entry 1MKG
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 CYS 51 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C LEU* 4.5 7.9 - - - -
33C VAL 3.3 17.5 - - - +
34C ASP* 3.5 13.0 - - + +
35C ILE* 3.9 1.8 - - - +
49C PRO* 3.2 8.3 - - - +
50C SER* 1.3 79.6 - - - +
52C VAL* 1.3 63.5 + - - +
24D SER* 2.8 33.9 + - - -
59D GLY* 3.8 7.9 - - - -
60D CYS* 2.1 57.8 - - + -
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.4 4.6 - - - -
33C VAL* 2.7 42.1 + - + +
35C ILE* 4.0 7.9 - - + -
49C PRO* 5.0 0.4 - - + -
51C CYS* 1.3 76.5 - - - +
53C PRO* 1.3 65.2 - - + +
54C LEU* 3.3 24.5 + - + -
78C MET* 3.7 15.5 - - - -
80C ILE* 3.9 7.9 - - + -
96C PHE* 3.8 36.3 - - + -
20D VAL* 3.6 24.9 - - + -
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Residues in contact with PRO 53 (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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30C GLU* 3.8 29.1 - - + +
31C THR 3.7 5.4 - - - +
32C LEU* 3.9 15.0 - - + -
52C VAL* 1.3 84.3 - - + +
54C LEU* 1.3 65.7 + - - +
55C MET* 4.3 0.7 + - - +
76C ILE* 5.9 2.3 - - - +
78C MET* 3.9 17.2 - - + +
98C GLN* 4.8 4.0 + - - -
20D VAL* 4.3 8.5 - - + +
23D ARG* 3.5 40.1 + - + +
24D SER* 4.3 9.6 - - - -
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Residues in contact with LEU 54 (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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30C GLU* 4.4 1.8 - - - -
31C THR* 2.7 45.9 + - - +
33C VAL* 3.8 24.7 - - + -
38C GLU* 4.4 2.2 - - - +
52C VAL* 3.9 19.1 - - + +
53C PRO* 1.3 78.9 - - - +
55C MET* 1.3 62.3 + - - +
56C ARG* 3.3 37.5 + - + +
76C ILE* 4.0 19.1 - - + -
78C MET* 4.8 2.5 - - - -
96C PHE* 3.6 33.2 - - + -
97C LEU 3.8 4.7 - - - +
98C GLN* 4.3 5.8 - - + +
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Residues in contact with MET 55 (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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28C PRO* 3.8 28.3 - - + +
29C ILE* 3.8 0.9 - - - -
30C GLU* 3.6 33.2 - - - +
54C LEU* 1.3 70.5 - - - +
56C ARG* 1.3 64.2 + - - +
98C GLN* 3.2 28.1 - - - +
99C HIS 2.9 41.5 + - - +
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Residues in contact with ARG 56 (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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28C PRO* 3.7 4.9 - - - -
29C ILE* 2.7 38.8 + - - +
31C THR* 3.8 21.3 - - + +
33C VAL* 4.5 10.8 - - + +
37C GLN* 4.7 5.5 - - - +
38C GLU* 3.2 32.7 + - - -
54C LEU* 3.3 25.2 + - + +
55C MET* 1.3 84.2 + - - +
57C ALA* 1.3 70.2 + - - +
58C GLY 3.3 0.3 + - - -
97C LEU* 2.7 40.8 + - - +
99C HIS* 3.4 29.5 + - + +
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Residues in contact with ALA 57 (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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27C HIS 3.9 4.9 - - - -
28C PRO* 4.2 0.7 - - - -
29C ILE* 5.2 0.2 - - - -
31C THR* 5.6 0.2 + - - -
56C ARG* 1.3 74.7 - - - +
58C GLY* 1.3 58.4 + - - +
68C CYS* 4.1 15.4 - - - +
69C VAL 4.2 0.9 - - - -
70C PRO* 4.0 17.3 - - + -
99C HIS* 2.9 22.0 + - + +
102C ALA* 3.7 26.5 - - + -
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Residues in contact with GLY 58 (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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26C CYS* 3.3 2.6 - - - -
27C HIS* 2.9 38.9 + - - +
29C ILE* 4.5 6.3 - - - -
56C ARG 3.3 2.0 + - - -
57C ALA* 1.3 75.8 - - - +
59C GLY* 1.3 60.4 + - - -
68C CYS* 3.5 6.8 - - - -
32D LEU* 3.6 12.6 - - - -
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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