Contacts of the strand formed by residues 193 - 198 (chain A) in PDB entry 1ASZ
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 LYS 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ASP 4.9 1.3 - - - -
74A ASN* 3.0 37.9 - - - +
108A GLU* 4.5 8.1 + - - -
148A THR* 6.2 0.4 - - - -
168A VAL* 3.5 0.9 - - - -
169A ARG* 2.7 71.2 + - + +
191A ILE* 3.8 1.0 - - - +
192A THR* 1.3 94.8 + - - +
194A ILE* 1.3 60.0 + - - +
195A TYR* 3.3 29.7 - - + +
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Residues in contact with ILE 194 (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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74A ASN 2.9 5.9 + - - +
75A TYR* 3.2 16.2 - - + -
128A LEU* 3.7 24.5 - - + -
141A VAL* 4.7 1.1 - - + -
153A MET* 4.5 9.6 - - + -
156A TRP* 2.9 40.5 - - + -
157A ALA* 4.3 10.1 - - + -
160A LEU* 3.7 26.9 - - + -
166A VAL* 4.5 7.4 - - + -
167A LEU 4.0 2.7 - - - -
168A VAL* 3.6 21.5 - - + -
191A ILE* 3.8 20.6 - - + -
193A LYS* 1.3 75.7 - - - +
195A TYR* 1.3 64.1 + - - +
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Residues in contact with TYR 195 (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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72A LYS 5.5 0.2 - - - -
73A ASP* 3.0 22.8 + - - -
74A ASN* 3.3 11.8 - - - -
75A TYR* 3.2 22.4 - - - -
76A GLY* 2.8 33.4 - - - +
78A LEU* 3.8 31.6 - - + -
156A TRP* 4.5 0.2 - - - -
166A VAL* 3.4 5.1 - - - +
167A LEU* 3.0 48.6 + - + +
169A ARG* 5.6 1.1 - - + -
193A LYS* 3.3 34.9 - - + +
194A ILE* 1.3 74.7 - - - +
196A THR* 1.3 62.5 + - - +
197A ILE* 4.0 0.3 - - - +
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Residues in contact with THR 196 (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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76A GLY 2.7 7.3 + - - -
77A LYS* 3.3 18.2 - - - +
78A LEU* 3.1 25.3 + - - +
156A TRP* 3.6 19.7 - - + -
160A LEU* 3.4 33.0 - - + -
165A ILE 3.7 4.9 - - - -
166A VAL* 4.0 7.2 - - + -
195A TYR* 1.3 74.3 - - - +
197A ILE* 1.3 59.5 + - - +
198A SER 3.5 6.5 - - - +
199A GLU* 2.5 32.7 + - - +
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Residues in contact with ILE 197 (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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78A LEU* 4.5 12.6 - - + +
81A ILE* 4.3 27.9 - - + +
93A ARG* 5.2 5.6 - - - +
112A ARG* 3.3 34.8 - - + -
165A ILE* 3.0 18.8 + - + -
167A LEU* 3.4 43.5 - - + +
195A TYR 4.0 0.7 - - - +
196A THR* 1.3 76.0 - - - +
198A SER* 1.3 62.3 + - - +
348B GLU 5.5 2.0 - - - +
487B HIS* 4.9 9.2 + - - -
519B CYS 4.6 2.4 - - - +
520B PRO* 5.4 0.4 - - + -
521B PRO* 4.6 11.6 - - + +
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Residues in contact with SER 198 (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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77A LYS* 6.0 0.4 - - - +
164A SER* 3.4 5.3 - - - -
165A ILE* 3.1 45.0 + - - +
196A THR* 3.5 2.3 - - - -
197A ILE* 1.3 81.3 + - - +
199A GLU* 1.3 67.9 + - - +
487B HIS* 5.2 3.1 - - - -
518B GLY* 3.6 5.4 - - - -
519B CYS 3.1 34.9 + - - -
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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