Contacts of the strand formed by residues 73 - 80 (chain A) in PDB entry 5K79
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 TYR 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A PHE* 4.8 11.4 - + + -
5A SER* 3.5 32.3 - - - -
11A ILE* 3.9 32.5 - - + +
64A LEU* 4.4 18.8 - - + -
65A ALA 3.6 6.3 - - - -
66A GLN* 3.6 38.7 + - + +
71A ARG 4.6 4.5 - - - -
72A THR* 1.3 71.4 - - - +
74A VAL* 1.3 58.1 + - - +
93A GLU* 3.5 5.7 - - - +
94A LEU* 2.9 29.3 + - + -
95A ASP* 4.2 14.8 + - - +
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Residues in contact with VAL 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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64A LEU* 3.4 7.7 - - - +
65A ALA* 2.8 56.2 + - + +
67A SER* 4.1 7.4 - - - +
72A THR* 3.6 21.1 - - - +
73A TYR* 1.3 79.5 - - - +
75A LEU* 1.3 63.9 + - - +
76A ALA* 4.6 3.1 - - + -
91A GLU* 3.8 41.1 - - + +
92A ILE 3.2 13.2 - - - +
93A GLU* 4.0 10.5 - - + -
94A LEU* 4.0 5.6 - - - -
1B THR* 5.8 0.2 - - - +
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Residues in contact with LEU 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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13A LEU* 3.9 12.6 - - + -
37A LEU* 4.2 9.0 - - + -
41A ILE* 4.0 23.3 - - + -
48A LEU* 3.5 15.2 - - + +
55A PHE* 3.5 35.4 - - + -
62A ILE* 3.7 29.6 - - + -
63A GLY 3.6 9.6 - - - +
64A LEU* 4.9 1.1 - - + +
74A VAL* 1.3 71.7 - - - +
76A ALA* 1.3 60.7 + - - +
91A GLU* 3.3 2.9 - - - -
92A ILE* 2.9 45.2 + - + -
94A LEU* 3.8 17.3 - - + +
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Residues in contact with ALA 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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61A SER 3.5 2.3 - - - +
62A ILE* 3.4 2.1 - - - +
63A GLY* 2.9 38.7 + - - +
65A ALA* 5.1 7.6 - - + -
74A VAL* 3.8 8.0 + - + -
75A LEU* 1.3 76.5 - - - +
77A ALA* 1.3 63.7 + - - +
90A THR 3.4 8.7 - - - +
91A GLU* 3.9 17.5 - - + +
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Residues in contact with ALA 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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48A LEU* 4.4 8.7 - - + +
55A PHE* 5.3 1.8 - - + -
59A CYS* 4.0 14.1 - - + -
60A ASP 3.5 9.9 - - - +
61A SER 3.6 8.7 - - - -
62A ILE* 3.9 17.3 - - + -
75A LEU* 5.6 0.2 - - + -
76A ALA* 1.3 76.5 - - - +
78A GLU* 1.3 65.2 + - - +
79A CYS* 3.9 7.9 - - - -
89A PRO* 3.5 4.7 - - - +
90A THR* 2.9 32.0 + - - -
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Residues in contact with GLU 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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59A CYS* 3.4 0.7 - - - -
60A ASP* 2.8 43.1 + - + +
61A SER* 4.1 18.2 - - - +
77A ALA* 1.3 73.0 - - - +
79A CYS* 1.3 61.1 + - - +
87A TYR* 3.5 18.5 - - + +
88A ILE* 3.6 5.0 + - - -
89A PRO* 3.4 25.0 - - - +
70B THR* 5.5 5.3 - - + -
72B THR* 3.8 10.3 - - - +
93B GLU* 2.5 39.1 - - - +
96B GLU* 4.4 3.3 - - - +
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Residues in contact with CYS 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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43A ASN* 3.6 13.5 - - - +
46A GLY* 3.7 18.8 - - - +
48A LEU* 3.7 13.7 - - - -
58A THR 3.8 0.2 - - - -
59A CYS* 2.0 47.1 - - - -
77A ALA* 4.1 2.5 - - - -
78A GLU* 1.3 73.5 - - - +
80A GLU* 1.3 63.4 + - - +
81A ARG 3.6 0.7 + - - -
87A TYR* 3.3 4.6 - - - -
88A ILE* 2.9 34.3 + - - +
90A THR* 3.4 20.6 - - + -
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Residues in contact with GLU 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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43A ASN* 2.9 20.2 + - - +
45A ASP* 4.5 0.7 - - - -
46A GLY 3.4 7.5 + - - -
58A THR* 2.9 38.9 + - - +
79A CYS* 1.3 71.8 - - - +
81A ARG* 1.3 72.4 + - - +
84A GLY* 2.9 36.2 - - - +
86A THR 3.7 4.5 - - - +
87A TYR* 3.6 34.0 + - + +
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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