Contacts of the strand formed by residues 194 - 198 (chain C) in PDB entry 1D1T
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 THR 194 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C GLY 4.6 2.8 + - - -
193C SER* 1.3 75.1 + - - +
195C CYS* 1.3 66.3 + - - +
196C VAL* 5.4 0.2 - - + -
218C ARG* 3.2 30.2 - - + +
220C ILE* 4.7 3.1 - - + -
258C THR* 3.6 31.5 - - + +
261C ASN* 3.8 26.9 + - - +
262C VAL* 3.9 6.5 - - + -
263C GLY* 3.1 23.1 + - - +
264C TYR* 3.2 7.8 + - - +
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Residues in contact with CYS 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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189C VAL* 3.3 39.0 - - - -
193C SER* 4.5 0.4 - - - -
194C THR* 1.3 77.4 - - - +
196C VAL* 1.3 71.2 + - - +
211C CYS* 3.6 26.5 - - - -
216C ALA* 3.9 9.9 - - - -
218C ARG 2.8 10.0 + - - +
219C ILE* 3.6 10.0 - - + -
220C ILE* 3.1 23.2 + - - +
264C TYR* 3.4 18.8 - - + -
266C PHE* 4.4 2.9 - - + -
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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
----------------------------------------------------------
194C THR* 5.4 0.7 - - + -
195C CYS* 1.3 79.2 - - - +
197C VAL* 1.3 66.0 + - - +
198C PHE* 3.5 25.1 - - + -
220C ILE* 3.3 16.8 - - + +
222C ILE* 3.9 17.9 - - + -
254C LEU* 3.8 24.5 - - + -
262C VAL* 3.6 27.6 - - + -
264C TYR 3.0 9.0 + - - +
265C THR* 3.8 8.5 - - + -
266C PHE* 3.0 32.7 + - - -
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Residues in contact with VAL 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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196C VAL* 1.3 80.2 - - - +
198C PHE* 1.3 63.2 + - - +
199C GLY 3.5 19.2 + - - +
200C LEU* 4.4 2.6 - - + +
204C GLY* 3.9 7.2 - - - +
207C VAL* 3.2 37.5 - - + -
208C ILE* 3.9 21.1 - - + +
211C CYS* 5.0 3.4 - - - -
219C ILE* 4.3 13.5 - - + -
220C ILE 3.0 11.0 + - - +
221C GLY* 3.8 3.3 - - - -
222C ILE* 2.7 32.2 + - - +
266C PHE* 3.9 9.4 - - + -
268C VAL* 4.4 3.4 - - + -
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Residues in contact with PHE 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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196C VAL* 3.5 20.0 - - + -
197C VAL* 1.3 74.5 - - - +
199C GLY* 1.3 62.2 + - - +
222C ILE* 3.7 36.6 - - + -
243C PRO* 5.9 2.7 - - + -
250C ILE* 4.2 10.5 - - + -
254C LEU* 4.0 3.4 - - + -
265C THR* 4.2 6.7 - - + -
266C PHE 2.9 23.3 + - - +
267C GLU* 4.2 7.4 - - + -
268C VAL* 3.0 28.6 + - - +
269C ILE* 3.9 15.7 - - + -
274C THR* 4.7 16.6 - - + +
277C ASP* 4.1 18.6 - - + -
278C ALA* 3.7 28.9 - - + -
281C SER* 3.9 17.7 - - - -
3377C NAD 5.5 0.9 - + - -
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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