Contacts of the strand formed by residues 195 - 201 (chain C) in PDB entry 3DUF
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 195 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151C ALA* 4.6 7.0 - - + +
155C ALA* 3.7 18.8 - - + -
167C ALA* 3.3 8.7 - - + +
188C ALA* 4.6 4.0 - - + -
193C ALA 2.9 9.8 + - - +
194C PRO* 1.3 75.2 - - - +
196C ILE* 1.3 63.9 + - - +
197C PHE* 3.9 28.3 - - + -
252C ALA* 4.7 1.3 - - - +
257C GLY 4.6 0.5 - - - +
258C PRO* 3.0 29.3 - - + +
259C THR 3.4 2.6 + - - -
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Residues in contact with ILE 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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92C LEU* 4.9 0.9 - - + -
166C VAL* 4.0 22.0 - - + -
167C ALA 2.9 11.5 + - - +
168C ILE* 3.4 13.2 - - + +
169C THR* 3.1 28.1 + - - +
195C ALA* 1.3 78.1 - - - +
197C PHE* 1.3 63.7 + - - +
198C VAL* 4.0 20.2 - - + -
245C VAL* 4.3 12.6 - - + +
248C ALA* 4.0 18.4 - - + +
249C ARG* 3.7 34.3 - - + +
252C ALA* 5.1 2.9 - - + -
259C THR 3.7 6.7 - - - +
261C ILE* 4.2 20.0 - - + -
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Residues in contact with PHE 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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148C TYR* 3.5 51.6 - + + -
151C ALA* 4.3 5.2 - - + -
152C ALA 4.9 3.1 - - - -
169C THR* 3.5 16.8 - - + -
184C GLY 3.8 9.4 - - - -
185C ILE* 3.8 20.9 - - + -
188C ALA* 3.6 33.0 - - + -
195C ALA* 3.9 17.0 - - + -
196C ILE* 1.3 74.4 - - - +
198C VAL* 1.3 57.2 + - - +
228C ILE* 4.7 2.2 - - + -
258C PRO* 4.0 11.2 - - + -
259C THR 2.9 18.3 + - - +
260C LEU* 3.3 20.5 - - + +
261C ILE* 2.7 33.1 + - - +
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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
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84C SER* 5.0 3.6 - - - +
88C SER* 5.5 2.5 - - - -
148C TYR* 3.1 12.4 + - - -
168C ILE* 4.0 17.5 - - + -
169C THR 2.9 17.2 + - - +
170C TYR* 3.4 29.8 - - + +
171C THR 3.2 18.9 + - - -
196C ILE* 4.0 18.8 - - + -
197C PHE* 1.3 76.8 - - - +
199C VAL* 1.3 67.8 + - - +
200C GLN* 4.4 5.8 - - + -
245C VAL* 5.1 6.1 - - + -
261C ILE* 3.4 18.6 - - + +
263C THR* 4.6 13.5 - - + -
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Residues in contact with VAL 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C TYR* 3.5 17.5 - - - +
171C THR* 3.7 5.4 - - + -
172C GLY 4.0 10.5 - - - +
176C THR* 4.0 24.7 - - + -
181C PHE* 4.1 3.4 - - + -
198C VAL* 1.3 72.7 - - - +
200C GLN* 1.3 58.4 + - - +
201C ASN 3.6 5.0 + - - +
219C LEU* 4.0 29.6 - - + +
260C LEU* 3.7 22.2 - - + -
261C ILE 2.6 14.6 + - - +
262C GLU* 4.1 10.8 - - + -
263C THR* 2.7 33.6 + - - +
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Residues in contact with GLN 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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81C GLN* 3.7 21.0 + - - +
84C SER* 2.8 27.7 + - - +
85C GLN* 3.3 26.1 - - - +
103C ARG* 5.8 2.8 - - - +
104C ASP* 2.8 31.1 + - - -
170C TYR* 4.0 14.4 - - + +
171C THR 2.9 17.4 + - - +
172C GLY* 3.6 11.0 - - - -
173C ASP* 3.6 7.3 - - - +
198C VAL* 4.4 9.4 - - + -
199C VAL* 1.3 75.4 - - - +
201C ASN* 1.3 59.9 + - - +
202C ASN* 3.2 10.4 + - - +
263C THR* 3.5 8.7 - - - +
265C CYS* 4.2 3.4 - - - -
1368C MG 3.9 2.8 - - - -
1370C R1T 5.2 2.5 + - - +
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Residues in contact with ASN 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 ASP* 3.4 16.7 - - - +
199C VAL* 3.6 1.4 + - - +
200C GLN* 1.3 68.8 - - - +
202C ASN* 1.3 58.3 + - - +
203C ARG* 3.0 33.7 + - - +
210C VAL* 4.1 10.0 - - - +
219C LEU* 3.6 25.4 - - + +
262C GLU* 3.4 23.2 + - + +
263C THR 2.9 18.2 + - - +
264C LEU* 3.8 14.8 - - + +
265C CYS* 3.0 25.0 + - - +
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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