Contacts of the strand formed by residues 71 - 76 (chain P) in PDB entry 5A0Q
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 ILE 71 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66P PRO* 3.6 4.3 - - - +
67P ILE* 3.2 29.2 + - + -
68P THR* 3.0 30.6 + - + +
70P HIS* 1.3 83.6 - - - +
72P GLY* 1.3 82.1 + - - +
104P ILE 4.3 7.6 - - - +
106P THR* 3.4 44.4 - - + +
109P LEU* 4.1 22.2 - - + -
135P ILE* 3.5 18.2 - - + -
136P CYS 3.7 6.3 - - - +
137P GLY* 4.4 1.1 - - - -
138P TRP 5.5 0.2 - - - +
139P ASN* 6.3 0.9 - - - +
217P PHE* 3.9 9.4 - - - -
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Residues in contact with GLY 72 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P LEU* 4.7 3.4 - - - -
64P VAL* 5.8 0.2 - - - -
65P GLU 3.7 11.7 - - - -
66P PRO* 4.2 1.3 - - - -
67P ILE* 4.1 1.8 - - - -
71P ILE* 1.3 85.3 - - - +
73P LEU* 1.3 62.8 + - - -
135P ILE* 3.4 5.0 - - - +
136P CYS 3.3 27.3 + - - -
217P PHE* 3.8 19.7 - - - -
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Residues in contact with LEU 73 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P LEU* 4.0 2.2 - - - +
63P LYS 3.1 11.2 - - - +
64P VAL* 3.3 11.6 - - - +
65P GLU 3.5 5.2 + - - +
67P ILE* 3.4 31.9 - - + -
72P GLY* 1.3 71.7 - - - -
74P VAL* 1.3 68.9 + - - +
82P TYR* 3.4 19.5 - - + +
85P LEU* 4.5 3.1 - - + -
86P VAL* 3.7 28.0 - - + -
89P ALA* 4.6 6.3 - - + -
113P VAL* 6.2 0.2 - - + -
133P LEU* 2.8 42.8 - - + -
134P LEU 3.3 3.8 - - - -
135P ILE* 3.4 24.9 - - + -
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Residues in contact with VAL 74 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34P SER* 3.4 31.2 - - - +
35P VAL 5.3 0.4 - - - +
45P LEU* 3.5 35.9 - - + +
46P ALA 4.3 4.0 - - - +
47P THR* 4.1 17.3 - - + -
63P LYS* 3.4 7.2 - - + +
64P VAL* 3.9 25.4 - - + -
73P LEU* 1.3 78.7 - - - +
75P TYR* 1.4 64.8 + - - +
133P LEU* 3.1 3.8 - - - -
134P LEU* 2.9 34.7 + - + +
162P MET* 3.5 2.0 - - + +
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Residues in contact with TYR 75 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159O TYR* 5.6 2.9 - - - -
32P ALA 4.7 0.2 - - - +
34P SER* 3.2 15.4 + - - -
47P THR* 4.6 0.2 + - - -
61P VAL* 5.2 7.9 - - + +
62P HIS 5.0 0.9 - - - -
63P LYS* 3.4 66.5 + - + +
74P VAL* 1.4 73.9 - - - +
76P SER* 1.3 68.3 + - - +
77P GLY 3.7 11.0 - - - -
78P MET 3.9 11.4 - - - -
79P GLY* 3.5 32.9 - - - -
82P TYR* 3.2 53.2 - + + -
83P ARG* 4.9 3.6 + - - -
131P VAL* 3.9 9.0 - - + -
132P SER 3.5 9.2 - - - +
133P LEU* 3.9 1.1 - - + -
162P MET* 4.2 0.7 - - - -
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Residues in contact with SER 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P VAL* 3.6 16.3 - - - +
30P GLY 4.5 0.4 - - - -
31P GLY* 5.1 0.7 - - - -
32P ALA 3.9 11.2 - - - +
34P SER* 4.0 5.2 - - - -
63P LYS* 5.5 0.7 - - - +
75P TYR* 1.3 78.2 - - - +
77P GLY* 1.3 60.3 + - - +
131P VAL* 3.6 2.4 - - - -
132P SER* 2.9 34.3 + - - +
162P MET* 3.4 11.3 - - - +
163P GLY* 3.4 38.2 + - - -
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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