Contacts of the strand formed by residues 78 - 83 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I TYR* 3.0 4.9 - - - -
75I ILE 2.8 35.4 + - - +
76I GLY 3.4 13.2 - - - -
77I ARG* 1.3 83.9 - - + +
79I LYS* 1.3 61.2 + - - +
119I LEU* 3.4 9.7 - - + +
120I ARG* 3.5 47.6 + - + +
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Residues in contact with LYS 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I GLU* 3.6 19.6 + - - -
72I SER* 4.0 6.5 - - - +
73I LEU 3.2 9.9 - - - +
74I TYR* 3.6 39.4 + - + +
77I ARG 4.0 0.6 + - - +
78I HIS* 1.3 77.0 - - - +
80I VAL* 1.3 67.7 + - - +
81I THR* 3.7 23.8 + - - +
119I LEU* 3.9 3.5 - - - +
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Residues in contact with VAL 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H PRO 5.0 1.3 - - - +
71I TYR 4.0 0.2 - - - +
72I SER* 3.1 4.9 - - - -
73I LEU* 2.9 46.2 + - + +
79I LYS* 1.3 79.4 - - - +
81I THR* 1.3 64.7 + - - +
105I ALA* 3.9 26.9 - - + -
107I PHE* 4.9 4.4 - - + -
117I LYS* 3.7 24.9 - - + -
118I GLY 3.5 26.2 - - - +
119I LEU* 3.9 14.8 - - + -
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Residues in contact with THR 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H ASP* 4.9 0.3 - - - -
66I GLU* 4.4 3.7 - - + +
70I GLU* 4.1 31.2 - - + +
71I TYR 3.3 10.3 - - - +
72I SER* 2.6 26.3 + - - +
79I LYS* 3.7 17.4 - - - -
80I VAL* 1.3 75.2 - - - +
82I SER* 1.3 64.7 + - - +
83I LYS* 5.6 2.0 - - + +
117I LYS* 2.9 25.5 + - - +
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Residues in contact with SER 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H ASP* 3.4 9.8 + - - -
69I GLY 4.0 0.2 - - - +
70I GLU* 3.6 1.9 - - - -
71I TYR* 2.9 34.6 + - - +
81I THR* 1.3 71.6 + - - +
83I LYS* 1.3 64.7 + - - +
107I PHE* 4.5 10.9 - - - -
114I LEU* 3.8 26.0 - - - +
115I VAL 2.8 26.9 + - - -
117I LYS* 3.4 15.6 - - - +
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Residues in contact with LYS 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H TYR* 5.1 2.4 + - - -
42H ASP* 2.9 48.2 + - + +
43H LEU* 5.1 0.4 - - - +
44H SER* 3.6 21.6 + - - +
88H PHE* 4.2 13.9 - - + -
89H PRO* 3.6 18.4 - - + +
69I GLY 3.2 5.2 - - - +
70I GLU* 3.7 36.6 - - + +
81I THR* 5.6 2.2 - - + +
82I SER* 1.3 75.9 - - - +
84I VAL* 1.3 64.3 + - - +
114I LEU* 3.7 14.0 - - - +
115I VAL* 5.2 1.6 + - - +
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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