Contacts of the strand formed by residues 197 - 203 (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 197 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153C ALA* 4.6 5.8 - - + +
154C ALA* 5.0 0.2 - - - -
157C ALA* 3.6 19.5 - - + -
169C ALA 3.1 9.4 - - - +
171C CYS* 6.3 0.4 - - + -
190C ALA* 4.7 4.3 - - + -
195C ALA 2.8 9.5 + - - +
196C PRO* 1.3 73.5 - - - +
198C VAL* 1.3 64.7 + - - +
199C PHE* 3.8 28.5 - - + -
254C ALA* 4.1 1.2 - - - +
260C PRO* 3.0 31.9 - - + +
261C SER 3.6 0.3 + - - -
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Residues in contact with VAL 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C VAL* 4.3 4.5 - - + -
169C ALA 2.9 7.3 + - - -
170C VAL* 3.4 12.7 - - + +
171C CYS* 2.9 25.8 + - - +
197C ALA* 1.3 78.3 - - - +
199C PHE* 1.3 63.6 + - - +
200C ILE* 3.8 23.2 + - + +
247C VAL* 5.0 4.3 - - + -
250C ALA* 3.6 49.1 - - + +
251C VAL* 3.8 14.4 - - + +
254C ALA* 4.1 6.7 - - + -
261C SER 3.9 7.4 - - - +
263C VAL* 4.3 9.4 - - + -
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Residues in contact with PHE 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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150C VAL* 3.9 20.2 - - + -
153C ALA* 4.4 3.6 - - + -
154C ALA* 4.5 7.0 - - + -
171C CYS* 3.5 29.2 - - + -
173C PHE* 3.8 12.6 - + + -
187C ILE* 3.7 41.5 - - + -
190C ALA* 3.8 24.5 - - + -
197C ALA* 3.8 28.5 - - + -
198C VAL* 1.3 72.0 - - - +
200C ILE* 1.3 60.9 + - - +
230C ILE* 5.2 0.7 - - + -
260C PRO* 3.9 10.5 - - + -
261C SER 3.0 17.6 + - - +
262C LEU* 3.3 16.3 - - + +
263C VAL 2.8 25.8 + - - -
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Residues in contact with ILE 200 (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* 3.9 27.4 - - + -
170C VAL* 4.5 12.6 - - + -
171C CYS 2.8 11.8 + - - +
172C THR* 3.3 10.8 - - + +
173C PHE* 3.1 28.9 + - - +
198C VAL* 3.8 20.2 - - + +
199C PHE* 1.3 78.3 - - - +
201C ALA* 1.3 62.5 + - - +
202C GLU* 3.8 1.5 + - + -
247C VAL* 3.8 29.2 - - + -
263C VAL* 3.3 16.6 - - + +
265C LEU* 3.5 32.8 - - + -
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Residues in contact with ALA 201 (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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173C PHE* 3.3 27.2 - - + +
174C GLY 4.9 1.6 - - - +
199C PHE 4.2 0.2 - - - -
200C ILE* 1.3 73.4 - - - +
202C GLU* 1.3 61.0 + - - +
203C ASN 3.3 1.9 + - - +
221C ILE* 4.0 36.6 - - + -
262C LEU* 5.0 0.9 - - + +
263C VAL 2.8 13.4 + - - +
264C GLU* 4.3 4.3 - - + -
265C LEU* 2.8 35.5 + - - +
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Residues in contact with GLU 202 (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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73C HIS* 2.9 39.6 + - + +
76C ALA* 4.6 13.9 - - + -
77C GLN* 3.0 25.0 + - - +
80C ILE* 4.7 7.6 - - + +
94C TYR* 3.6 15.8 + - - +
97C ASP* 2.5 29.6 - - - +
172C THR* 3.5 16.0 - - - +
173C PHE 2.7 14.1 + - - +
174C GLY* 3.5 16.4 - - - -
175C ASP* 3.9 1.1 + - - +
200C ILE* 4.9 3.8 - - + +
201C ALA* 1.3 70.7 - - - +
203C ASN* 1.3 59.9 + - - +
204C ASN* 3.4 7.7 + - - -
265C LEU* 3.7 8.3 - - + -
267C VAL* 4.3 5.2 - - + -
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Residues in contact with ASN 203 (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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175C ASP* 3.2 24.2 - - - +
201C ALA 3.3 0.6 - - - +
202C GLU* 1.3 70.5 - - - +
204C ASN* 1.3 58.4 + - - +
205C PHE* 2.8 48.0 + - - -
212C TYR* 4.2 11.8 - - - -
221C ILE* 4.0 17.6 - - + +
264C GLU* 3.0 33.1 + - + +
265C LEU 3.0 12.4 + - - +
266C ARG* 3.6 3.6 - - - +
267C VAL* 2.9 27.3 + - - +
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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