Contacts of the strand formed by residues 72 - 78 (chain A) in PDB entry 2K9U
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 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A SER* 4.4 14.1 - - - -
42A TRP* 3.9 22.6 - - - +
66A GLU 4.3 2.4 - - - +
67A ASP* 4.8 2.1 - - - -
68A ARG 4.5 1.2 + - - -
69A LYS* 3.2 47.7 + - - +
71A GLY* 1.3 78.3 + - - +
73A CYS* 1.3 60.4 + - - +
74A GLY 3.5 0.7 + - - -
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Residues in contact with CYS 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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40A SER* 3.4 1.6 - - - -
41A ILE* 2.6 60.6 + - + +
43A THR* 4.9 11.0 - - + +
65A PHE* 4.5 23.3 - - - -
66A GLU 4.4 7.2 - - - -
67A ASP* 5.2 7.0 - - - +
69A LYS* 4.4 0.7 - - - -
71A GLY 3.9 2.2 + - - -
72A SER* 1.3 71.4 - - - +
74A GLY* 1.3 63.3 + - - +
75A VAL* 3.6 9.4 + - - -
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Residues in contact with GLY 74 (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 GLU* 5.6 4.3 - - - -
39A PHE 3.7 5.4 - - - -
64A ALA 3.0 4.3 - - - +
65A PHE* 3.3 0.4 - - - -
66A GLU* 2.7 44.2 + - - +
69A LYS* 3.2 27.3 - - - +
72A SER 3.5 2.2 + - - -
73A CYS* 1.3 70.8 - - - +
75A VAL* 1.3 63.1 + - - -
76A SER* 3.5 1.8 + - - -
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Residues in contact with VAL 75 (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 GLU* 3.6 1.6 - - - -
39A PHE* 3.1 57.1 + - + -
41A ILE* 3.3 33.4 - - + -
51A LEU* 6.0 3.6 - - + -
53A ILE* 5.3 8.5 - - + -
63A ILE* 3.6 32.3 - - + -
64A ALA 3.2 5.2 - - - +
65A PHE* 5.0 5.8 - - + +
73A CYS* 4.3 11.2 - - - +
74A GLY* 1.3 73.4 - - - -
76A SER* 1.3 61.1 + - - +
77A TYR* 3.7 1.5 + - + +
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Residues in contact with SER 76 (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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37A ALA 3.5 7.2 - - - -
38A GLU* 3.5 19.1 - - - -
62A GLU* 5.6 0.2 - - - +
63A ILE 3.0 1.7 - - - -
64A ALA* 2.4 66.9 + - - +
66A GLU* 5.0 6.8 + - - +
74A GLY 3.5 3.1 + - - -
75A VAL* 1.3 72.4 - - - +
77A TYR* 1.3 59.4 + - - +
78A VAL* 5.3 2.3 - - - +
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Residues in contact with TYR 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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27A GLY* 2.7 39.0 + - - -
30A ARG 3.9 6.6 + - - -
31A GLY* 4.8 1.2 - - - -
36A PRO* 4.0 0.2 - - - +
37A ALA* 2.7 62.5 + - + +
38A GLU 3.9 1.8 - - - -
39A PHE* 3.8 33.9 - + + -
61A ALA* 4.8 6.1 - - + -
62A GLU 2.9 21.3 - - - +
63A ILE* 4.3 7.2 - - + -
75A VAL* 4.0 1.3 - - + +
76A SER* 1.3 73.4 - - - +
78A VAL* 1.3 74.0 + - - +
79A VAL* 3.7 26.9 - - + -
103A VAL* 3.9 11.2 - - + +
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Residues in contact with VAL 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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34A GLY* 4.8 3.6 - - - -
35A VAL 4.2 6.3 - - - +
36A PRO* 4.1 30.1 - - + -
60A LYS 4.5 0.9 - - - +
61A ALA* 3.2 23.0 - - - -
62A GLU* 3.2 24.6 + - + -
76A SER* 5.3 2.0 - - - +
77A TYR* 1.3 87.3 - - - +
79A VAL* 1.3 73.0 + - - +
80A GLN 4.1 0.2 + - - -
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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