Contacts of the strand formed by residues 194 - 199 (chain A) in PDB entry 1UU1
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 LEU 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A ILE* 5.2 2.9 - - + -
164A LEU* 4.1 14.6 - - + -
169A PHE* 3.4 7.5 - - - -
170A VAL* 3.4 31.4 - - + +
172A LEU* 4.1 18.2 - - + -
184A TYR 4.1 4.0 - - - +
187A PHE* 3.4 35.0 - - + +
188A LEU* 3.4 38.6 - - + +
191A TYR* 4.4 9.2 - - + +
192A GLU 3.1 4.4 + - - +
193A ASN* 1.3 79.9 - - - +
195A ALA* 1.3 68.9 + - - +
196A VAL* 4.6 2.9 - - + -
216A ALA* 3.3 18.0 - - - +
217A SER 4.1 1.4 + - - -
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Residues in contact with ALA 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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92A MET* 4.1 12.6 - - + -
169A PHE* 3.5 22.2 - - + -
170A VAL 2.9 7.0 + - - +
171A ALA* 3.6 1.3 - - - -
172A LEU* 2.8 29.1 + - - +
194A LEU* 1.3 77.1 - - - +
196A VAL* 1.3 63.6 + - - +
197A ILE* 4.0 1.5 + - + +
214A VAL* 3.9 16.2 - - + -
215A VAL 3.4 5.6 - - - -
216A ALA* 3.7 11.7 - - + -
220A PHE* 4.1 1.8 - - + -
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Residues in contact with VAL 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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172A LEU* 3.4 22.2 - - + +
174A GLU* 3.4 38.1 - - + +
183A SER* 4.4 3.6 - - - +
184A TYR 4.3 2.0 - - - +
185A VAL* 3.8 28.7 - - + +
188A LEU* 4.3 11.4 - - + -
194A LEU* 4.6 3.4 - - + -
195A ALA* 1.3 75.9 - - - +
197A ILE* 1.3 64.4 + - - +
198A ARG* 4.5 9.9 - - + +
213A TYR 3.9 0.3 - - - +
214A VAL* 3.3 6.4 - - - +
215A VAL* 2.9 45.4 + - + +
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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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85A ALA* 3.9 25.8 - - + +
88A ILE* 3.9 25.8 - - + -
89A ILE* 4.2 18.2 - - + -
92A MET* 3.9 24.9 - - - -
143A PHE* 4.4 9.0 - - + -
171A ALA* 4.7 5.4 - - + -
172A LEU 2.7 17.2 + - - +
173A ASP* 3.8 15.2 - - - +
174A GLU* 2.7 35.0 + - - +
175A ALA 3.8 0.9 + - - -
195A ALA 4.5 5.2 - - - +
196A VAL* 1.3 77.6 - - - +
198A ARG* 1.3 64.5 + - - +
213A TYR 3.5 8.7 - - - +
214A VAL* 4.3 5.8 - - + -
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Residues in contact with ARG 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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68A TYR* 4.1 7.9 - - - -
69A LEU* 4.1 19.3 - - - +
85A ALA* 4.0 6.8 - - - +
174A GLU* 3.0 35.5 + - - -
175A ALA* 4.9 0.9 - - - +
177A TYR* 3.1 36.5 - - - -
178A GLU* 4.4 4.9 - - - +
183A SER* 3.2 33.5 + - - -
185A VAL* 5.0 6.2 - - - +
196A VAL* 4.5 10.9 - - + +
197A ILE* 1.3 78.2 - - - +
199A THR* 1.3 63.6 + - - +
212A GLY* 3.3 3.3 - - - -
213A TYR* 2.9 76.9 + - + +
215A VAL* 5.5 2.2 - - + -
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Residues in contact with THR 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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85A ALA* 3.9 5.4 - - + -
174A GLU 5.0 0.4 + - - -
175A ALA* 3.8 20.3 + - + +
178A GLU* 4.3 15.0 + - - +
198A ARG* 1.3 79.6 - - - +
200A PHE* 1.3 74.2 + - - +
201A SER* 2.9 11.7 + - - +
202A LYS* 3.6 33.3 + - + +
203A ALA 5.6 0.9 + - - -
204A PHE* 4.3 7.6 - - - -
211A VAL 3.3 9.6 + - - -
212A GLY* 4.0 0.9 - - - -
213A TYR* 4.4 6.0 - - - -
1335A PMP 2.5 31.2 + - - +
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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