Contacts of the strand formed by residues 196 - 201 (chain A) in PDB entry 1UA4
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 ASN 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLY 3.0 25.4 + - - -
85A LYS* 3.4 1.3 - - - +
86A ALA* 3.1 39.8 - - - +
180A GLU* 3.5 3.8 - - - +
181A PHE* 3.1 52.2 + - + +
194A ARG* 3.3 26.8 + - - +
195A GLU* 1.3 72.5 + - - +
197A ARG* 1.3 79.0 + - - +
293A GLU* 5.5 0.2 + - - -
435A THR* 3.4 14.6 + - - +
1456A AMP 4.7 2.8 + - - -
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Residues in contact with ARG 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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80A SER* 3.8 2.9 + - - -
86A ALA* 3.4 30.2 - - - +
87A ALA 3.3 21.7 + - - +
88A GLU* 5.6 2.4 + - - +
178A ILE* 3.8 21.1 - - + -
179A TYR 3.1 16.4 - - - +
180A GLU* 3.6 18.4 - - - +
181A PHE* 3.7 7.4 - - - -
196A ASN* 1.3 92.6 + - - +
198A PHE* 1.3 60.8 + - - +
199A ILE* 3.5 24.9 - - + +
435A THR* 3.4 15.0 - - - -
436A VAL* 4.2 13.3 - - + +
437A GLY 5.7 0.4 - - - +
1456A AMP 3.9 19.2 + - - -
1457A GLC 4.7 13.1 + - - -
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Residues in contact with PHE 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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63A LEU* 4.5 1.1 - - + -
67A ILE* 3.8 23.1 - - + -
73A LEU* 4.3 5.4 - - + -
76A SER* 3.4 39.3 - - - -
77A ILE* 3.7 35.7 - - + -
80A SER* 3.8 9.0 - - - +
87A ALA* 3.4 36.8 - - + -
88A GLU 4.0 2.0 - - - -
89A LEU* 3.8 17.7 - - + -
178A ILE* 3.8 0.3 - - - -
179A TYR* 2.9 41.2 + + + +
181A PHE* 4.4 1.0 - - + -
197A ARG* 1.3 75.8 - - - +
199A ILE* 1.3 82.3 + - - +
200A GLY* 4.0 3.6 - - - -
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Residues in contact with ILE 199 (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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87A ALA 3.0 7.1 + - - -
88A GLU* 3.2 29.7 - - + +
89A LEU 2.9 27.2 + - - +
176A HIS* 4.4 3.4 - - + -
177A TYR 3.4 3.6 - - - +
178A ILE* 3.6 37.2 - - + -
197A ARG* 3.5 36.6 - - - +
198A PHE* 1.3 83.8 - - - +
200A GLY* 1.3 67.5 + - - +
201A SER 4.2 0.4 - - - +
436A VAL* 4.3 4.5 - - + -
1457A GLC 3.9 30.7 - - - +
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Residues in contact with GLY 200 (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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67A ILE* 4.9 0.2 - - - -
89A LEU 3.5 6.5 - - - -
91A VAL* 3.8 16.2 - - - -
100A MET* 3.9 14.2 - - - +
177A TYR* 2.9 35.4 + - - -
179A TYR* 4.8 1.4 - - - -
198A PHE* 4.0 11.3 + - - -
199A ILE* 1.3 73.9 - - - +
201A SER* 1.3 64.1 + - - -
202A ALA 3.5 0.9 + - - -
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Residues in contact with SER 201 (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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88A GLU* 3.8 21.0 + - - +
89A LEU 3.0 8.0 + - - -
90A PHE* 3.2 31.1 + - - +
91A VAL* 2.9 26.3 + - - +
176A HIS* 3.8 26.9 - - - -
199A ILE* 3.8 2.6 - - - +
200A GLY* 1.3 70.7 - - - +
202A ALA* 1.3 60.6 + - - +
203A ASP 3.8 0.9 - - - -
207A THR* 3.9 10.0 - - - +
236A ALA* 5.7 2.2 - - - +
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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