Contacts of the strand formed by residues 194 - 199 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160C ILE* 5.1 1.3 - - + -
164C LEU* 3.9 22.0 - - + -
169C PHE* 3.5 5.1 - - - -
170C VAL* 3.5 28.0 - - + +
172C LEU* 4.1 22.7 - - + -
184C TYR* 4.0 11.4 - - + +
187C PHE* 3.7 33.9 - - + +
188C LEU* 3.2 35.4 - - + +
191C TYR* 4.2 6.3 - - + +
192C GLU 2.9 4.9 + - - +
193C ASN* 1.3 78.8 - - - +
195C ALA* 1.3 70.4 + - - +
196C VAL* 4.8 4.0 - - + +
216C ALA* 3.5 10.4 - - - +
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Residues in contact with ALA 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C MET* 4.0 24.0 - - + -
169C PHE* 3.3 23.3 - - + -
170C VAL 2.8 9.6 + - - +
171C ALA* 3.4 4.0 - - - -
172C LEU 2.7 32.9 + - - +
194C LEU* 1.3 79.0 - - - +
196C VAL* 1.3 58.7 + - - +
197C ILE* 3.9 1.4 + - - +
214C VAL* 4.5 1.6 - - + -
215C VAL 3.7 5.4 - - - +
216C ALA* 4.0 9.6 - - + -
220C PHE* 4.4 1.6 - - + -
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Residues in contact with VAL 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C LEU* 3.3 20.2 - - + -
174C GLU* 3.8 23.8 - - + +
184C TYR* 4.2 6.1 - - + +
185C VAL* 3.6 48.2 - - + +
188C LEU* 5.2 1.3 - - + +
194C LEU* 4.8 7.1 - - + +
195C ALA* 1.3 71.9 - - - +
197C ILE* 1.3 63.8 + - - +
198C ARG* 4.1 11.6 + - + +
213C TYR 4.1 0.2 - - - +
214C VAL* 3.6 3.3 - - - -
215C VAL* 3.0 39.5 + - + +
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Residues in contact with ILE 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ALA* 3.8 27.6 - - + +
88C ILE* 3.5 18.4 - - + -
89C ILE* 5.4 6.5 - - + -
92C MET* 3.3 37.7 - - + -
143C PHE* 6.2 0.4 - - + -
171C ALA* 5.0 6.1 - - + -
172C LEU 2.9 15.5 + - - +
173C ASP* 4.2 16.5 - - + +
174C GLU* 2.8 33.6 + - - +
175C ALA 3.8 0.7 + - - -
195C ALA 4.3 6.5 - - - +
196C VAL* 1.3 74.9 - - - +
198C ARG* 1.3 64.8 + - - +
213C TYR 3.7 8.3 - - - +
214C VAL* 3.5 16.8 - - + -
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Residues in contact with ARG 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C TYR* 4.0 7.1 - - - -
69C LEU* 4.0 18.7 - - - +
85C ALA* 4.0 8.2 - - - +
174C GLU* 2.6 42.3 + - - +
175C ALA* 5.3 0.7 - - - -
177C TYR* 3.4 36.5 - - - -
178C GLU* 4.8 2.9 - - - -
183C SER* 3.1 29.9 + - - -
185C VAL* 3.8 11.2 - - - +
196C VAL* 4.2 9.4 - - + +
197C ILE* 1.3 77.0 - - - +
199C THR* 1.3 59.5 + - - +
212C GLY* 3.1 4.3 - - - -
213C TYR* 2.8 85.7 + - + +
215C VAL* 5.5 0.4 - - + -
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Residues in contact with THR 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ALA* 4.3 4.9 - - - -
174C GLU 5.0 0.4 + - - -
175C ALA* 3.7 32.9 - - + +
178C GLU* 4.7 13.2 + - - +
198C ARG* 1.3 77.0 - - - +
200C PHE* 1.3 72.1 + - - +
201C SER* 3.0 14.4 + - - +
202C LYS* 4.0 22.9 - - + +
203C ALA* 5.5 1.4 + - - +
204C PHE* 4.6 6.6 - - - -
211C VAL 3.6 8.5 + - - -
212C GLY* 3.9 0.7 - - - -
213C TYR* 4.4 4.8 - - - -
1335C PMP 2.7 29.9 + - - +
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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