Contacts of the strand formed by residues 200 - 205 (chain C) in PDB entry 3L43
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 200 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C ILE* 3.5 16.5 - - - +
173C ALA* 4.3 13.0 - - + -
187C LEU* 4.8 1.3 - - + -
190C ALA* 3.7 25.3 + - + +
191C LYS* 6.5 0.4 - - + -
194C ASP* 2.8 29.8 + - - +
197C GLY* 3.8 13.0 + - - +
198C LEU 3.8 1.6 - - - -
199C ARG* 1.3 76.5 + - - +
201C ILE* 1.3 65.5 + - - +
202C GLY 4.3 0.2 - - - -
227C LEU* 4.4 27.6 - - + +
229C ARG* 3.3 24.6 + - - +
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Residues in contact with ILE 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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170C LEU* 4.0 19.5 - - + -
171C ILE 2.9 10.0 + - - +
172C LEU* 3.6 10.5 - - + +
173C ALA* 2.9 25.5 + - - +
200C THR* 1.3 79.7 - - - +
202C GLY* 1.3 69.8 + - - +
227C LEU* 4.4 1.1 - - - -
229C ARG* 3.7 33.4 - - + +
230C GLY 3.9 9.0 - - - +
232C VAL* 4.6 10.3 - - + -
277C LEU* 4.4 19.1 - - + -
280C VAL* 3.9 21.3 - - + +
281C LEU* 3.8 24.5 - - + -
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Residues in contact with GLY 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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173C ALA* 3.6 9.9 - - - -
187C LEU* 5.0 0.4 - - - -
201C ILE* 1.3 75.7 - - - +
203C VAL* 1.3 59.2 + - - +
227C LEU* 3.6 11.4 - - - +
230C GLY 3.1 11.1 + - - -
231C TYR* 3.3 26.3 - - - -
232C VAL* 2.8 30.4 + - - -
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Residues in contact with VAL 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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47C VAL* 4.5 4.3 - - + -
172C LEU* 3.7 32.1 - - + -
173C ALA 2.8 13.6 + - - +
174C VAL* 3.6 14.6 - - + -
175C THR 2.9 28.6 + - - +
201C ILE 4.4 1.3 - - - +
202C GLY* 1.3 78.0 - - - +
204C ILE* 1.3 66.4 + - - +
205C THR* 4.0 9.3 + - + -
231C TYR* 4.6 0.4 - - - -
232C VAL 3.3 7.9 - - - +
234C VAL* 3.9 28.5 - - + -
277C LEU* 3.9 25.8 - - + -
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Residues in contact with ILE 204 (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 ALA 5.5 0.2 - - - +
175C THR* 3.4 14.4 - - + +
177C ALA* 3.7 29.8 - - + -
181C LEU* 3.8 15.0 - - + -
203C VAL* 1.3 77.7 - - - +
205C THR* 1.3 57.7 + - - +
207C LEU* 3.4 19.6 - - + +
216C ALA* 4.6 5.4 - - + -
219C VAL* 3.8 15.3 - - + -
220C LEU* 3.8 27.4 - - + -
231C TYR* 3.6 32.3 - - + -
232C VAL 2.9 9.7 + - - -
233C GLY* 4.2 0.2 - - - -
234C VAL* 2.7 32.0 + - - +
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Residues in contact with THR 205 (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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42C ALA 2.7 22.5 + - - +
43C GLY 4.5 3.8 - - - +
47C VAL* 4.7 0.7 - - + -
174C VAL* 3.7 25.8 - - + -
175C THR 3.2 3.9 + - - -
176C PRO* 3.3 15.1 - - - +
177C ALA* 2.7 29.6 + - - +
203C VAL* 4.2 5.4 - - + -
204C ILE* 1.3 73.5 - - - +
206C LYS* 1.4 61.7 + - - +
207C LEU 3.1 4.9 + - - -
234C VAL* 3.5 27.1 - - + -
236C ASN* 3.9 17.7 - - - +
901C GDP 4.3 2.7 - - - -
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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