Contacts of the strand formed by residues 212 - 216 (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 GLY 212 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C VAL* 3.0 10.7 - - - +
82C GLY 2.8 30.7 + - - -
84C GLY 3.5 18.6 - - - +
85C ALA* 3.8 2.9 - - - -
88C ILE* 4.5 3.6 - - - -
198C ARG 3.1 13.5 - - - -
199C THR* 3.9 2.7 - - - -
211C VAL* 1.3 75.0 - - - +
213C TYR* 1.3 63.6 + - - -
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Residues in contact with TYR 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ILE* 3.7 39.3 - - + -
68C TYR* 3.4 19.6 - + - -
69C LEU* 4.2 8.7 - - + -
79C VAL* 4.5 2.2 - - + -
80C SER 3.2 15.5 - - - +
81C VAL* 4.0 6.7 - - + +
88C ILE* 4.4 1.3 - - - +
178C GLU* 4.4 2.3 + - - -
196C VAL 4.1 0.2 - - - +
197C ILE* 3.7 6.6 - - - +
198C ARG* 2.8 88.6 + - + +
199C THR 4.2 3.9 + - - -
200C PHE* 3.4 39.3 - + + -
204C PHE* 6.5 0.4 - + - -
212C GLY* 1.3 74.9 - - - +
214C VAL* 1.3 65.4 + - - +
215C VAL* 4.4 11.2 - - + -
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Residues in contact with VAL 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ASN 4.1 0.2 - - - -
79C VAL* 3.1 30.4 - - - +
80C SER 3.0 10.9 + - - +
88C ILE* 3.3 38.8 - - + -
92C MET* 3.9 11.9 - - + -
195C ALA* 4.5 2.2 - - + -
196C VAL 3.6 2.9 - - - +
197C ILE* 3.5 24.5 - - + -
213C TYR* 1.3 72.5 - - - +
215C VAL* 1.3 72.9 + - - +
216C ALA 4.2 0.2 - - - -
220C PHE* 4.0 13.0 - - + -
221C ILE* 4.2 9.0 - - + -
224C TYR* 4.1 19.1 - - + -
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Residues in contact with VAL 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 4.3 20.4 - - + -
74C LEU* 3.9 16.6 - - + -
78C ASN 3.1 9.6 - - - +
79C VAL* 4.6 8.7 - - + -
185C VAL* 3.8 15.0 - - + -
188C LEU* 3.3 27.2 - - + +
195C ALA* 3.7 0.3 - - - -
196C VAL* 3.0 47.5 + - + +
198C ARG* 5.5 0.2 - - + -
213C TYR* 4.4 15.7 - - + -
214C VAL* 1.3 79.4 - - - +
216C ALA* 1.3 63.4 + - - +
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Residues in contact with ALA 216 (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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78C ASN* 2.9 33.1 + - - +
188C LEU* 3.9 16.2 - - - -
194C LEU 3.5 14.4 - - - +
195C ALA* 4.0 5.4 - - + -
214C VAL* 4.8 0.2 - - + -
215C VAL* 1.3 78.0 - - - +
217C SER* 1.3 67.3 + - - +
220C PHE* 3.4 35.7 - - + -
221C ILE* 4.0 3.9 - - + +
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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