Contacts of the strand formed by residues 169 - 174 (chain C) in PDB entry 1UMD
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 ALA 169 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C TRP 3.4 4.7 - - - -
92C PHE* 4.2 16.6 - - + -
153C ALA* 4.0 21.7 - - + +
157C ALA* 4.2 5.2 - - + +
160C MET* 3.7 20.8 - - + -
168C VAL* 1.3 76.4 - - - +
170C VAL* 1.3 62.3 + - - +
171C CYS* 4.1 0.7 + - - +
196C PRO 3.0 9.4 + - - +
197C ALA* 3.1 5.4 - - + +
198C VAL 2.9 23.6 + - - -
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Residues in contact with VAL 170 (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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80C ILE* 4.5 10.5 - - + -
84C ILE* 3.6 31.9 - - + -
90C TRP 2.9 18.4 + - - +
91C VAL* 3.4 24.3 - - + +
92C PHE* 2.8 34.2 + - - +
168C VAL* 4.4 5.4 - - + +
169C ALA* 1.3 78.2 - - - +
171C CYS* 1.3 53.8 + - - +
172C THR* 4.2 2.0 - - + -
198C VAL* 3.4 15.3 - - + +
200C ILE* 4.5 14.1 - - + -
247C VAL* 5.4 0.4 - - + -
251C VAL* 4.2 15.9 - - + -
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Residues in contact with CYS 171 (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 PHE* 3.3 4.3 - - - +
149C HIS* 3.8 25.8 - - - -
150C VAL* 3.9 24.2 - - - -
153C ALA* 3.7 29.8 - - + -
169C ALA 5.4 0.7 - - - +
170C VAL* 1.3 74.3 - - - +
172C THR* 1.3 62.2 + - - +
173C PHE* 3.5 10.1 - - - -
198C VAL 2.9 9.0 + - - +
199C PHE* 3.8 17.3 - - + -
200C ILE* 2.8 27.9 + - - -
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Residues in contact with THR 172 (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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80C ILE* 3.6 33.7 - - + -
91C VAL* 5.1 2.6 - - + +
92C PHE 3.0 4.9 + - - +
93C PRO* 3.2 12.3 - - - +
94C TYR* 3.6 6.8 + - - -
97C ASP* 2.7 21.4 + - - -
100C LEU* 4.2 11.9 - - + +
149C HIS* 2.8 30.7 + - - -
170C VAL* 5.4 2.0 - - + -
171C CYS* 1.3 76.6 - - - +
173C PHE* 1.3 60.2 + - - +
200C ILE* 3.3 16.2 - - + +
202C GLU* 3.5 15.9 - - - +
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Residues in contact with PHE 173 (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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94C TYR* 3.6 17.4 - - - -
149C HIS* 4.2 11.4 - - + +
150C VAL* 4.4 5.6 - - + -
171C CYS* 3.5 31.6 - - - -
172C THR* 1.3 81.2 - - - +
174C GLY* 1.3 64.9 + - - +
177C ALA* 3.7 14.8 - - + -
178C THR* 3.9 7.6 - - + -
183C TRP* 3.2 34.8 - + - -
199C PHE* 3.8 11.9 - + + -
200C ILE 3.1 18.6 + - - -
201C ALA* 3.3 23.1 - - + -
202C GLU* 2.7 30.1 + - - +
262C LEU* 4.0 13.9 - - + -
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Residues in contact with GLY 174 (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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94C TYR* 3.8 11.6 - - - -
173C PHE* 1.3 85.6 - - - +
175C ASP* 1.3 66.3 + - - +
176C GLY 3.3 2.2 - - - -
177C ALA* 3.3 15.1 + - - +
178C THR* 3.9 2.1 + - - +
201C ALA* 5.0 0.9 - - - -
202C GLU 3.5 15.3 - - - -
2402C TPP 3.5 24.0 + - - -
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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