Contacts of the strand formed by residues 78 - 83 (chain P) in PDB entry 2A3W
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 HIS 78 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74P TYR* 3.0 5.6 - - - -
75P ILE 2.8 36.0 + - - +
76P GLY 3.1 15.4 + - - -
77P ARG* 1.3 83.1 - - + +
79P LYS* 1.3 59.9 + - - +
119P LEU* 3.3 11.5 - - + +
120P ARG* 3.7 38.7 + - + +
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Residues in contact with LYS 79 (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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66P GLU* 3.2 30.6 + - - -
72P SER* 4.2 0.9 - - - -
73P LEU 3.4 3.4 - - - +
74P TYR* 3.3 41.3 + - + -
77P ARG 4.9 0.9 - - - +
78P HIS* 1.3 78.5 - - - +
80P VAL* 1.3 76.2 + - - +
81P THR* 3.5 18.5 + - - +
119P LEU* 4.1 2.7 - - - +
346P CPJ 6.1 0.6 - - - -
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Residues in contact with VAL 80 (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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71P TYR 3.9 0.2 - - - +
72P SER* 3.1 5.9 - - - -
73P LEU* 2.9 52.6 + - + +
79P LYS* 1.3 79.7 - - - +
81P THR* 1.3 63.9 + - - +
105P ALA* 4.1 12.6 - - + -
107P PHE* 5.0 4.9 - - + -
117P LYS* 3.7 24.5 - - + -
118P GLY 3.5 26.5 - - - +
119P LEU* 3.8 24.0 - - + -
12T PRO 5.1 1.1 - - - +
13T ARG* 6.3 0.2 - - + -
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Residues in contact with THR 81 (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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66P GLU* 4.4 2.6 + - + -
70P GLU* 3.7 35.0 - - + +
71P TYR 3.3 8.7 - - - +
72P SER* 2.6 25.6 + - - +
79P LYS* 3.5 15.6 + - - +
80P VAL* 1.3 75.5 - - - +
82P SER* 1.3 63.8 + - - +
83P LYS* 5.5 5.1 - - + +
117P LYS* 2.9 25.9 + - - +
42T ASP* 4.3 0.5 - - - +
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Residues in contact with SER 82 (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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70P GLU* 3.7 1.9 - - - -
71P TYR* 3.0 31.3 + - - +
81P THR* 1.3 71.4 - - - +
83P LYS* 1.3 64.4 + - - +
107P PHE* 4.5 13.9 - - - -
114P LEU* 3.8 26.7 - - - +
115P VAL 2.7 27.7 + - - -
117P LYS* 3.5 18.4 + - - +
42T ASP* 3.4 5.9 + - - -
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Residues in contact with LYS 83 (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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69P GLY 3.2 5.6 - - - +
70P GLU* 3.5 38.5 + - + +
81P THR* 5.5 4.9 - - + -
82P SER* 1.3 75.6 - - - +
84P VAL* 1.3 63.9 + - - +
114P LEU* 3.7 15.4 - - - +
115P VAL* 5.3 1.6 + - - +
40T TYR* 5.2 2.1 + - - -
42T ASP* 2.9 46.0 + - + +
44T SER* 4.7 10.3 + - - -
88T PHE* 4.3 12.7 - - + -
89T PRO* 3.5 20.5 - - + +
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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