Contacts of the strand formed by residues 199 - 206 (chain C) in PDB entry 1A6Z
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 199 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C HIS* 4.4 3.6 - - + -
193C HIS 3.5 4.0 - - - +
194C VAL* 3.6 32.4 - - + +
198C VAL* 1.3 75.5 - - - +
200C THR* 1.3 65.0 + - - +
201C LEU* 4.1 14.8 - - + -
248C LEU 3.6 1.4 - - - +
249C ALA* 3.6 1.7 - - - -
250C VAL* 2.8 40.4 + - - +
252C PRO* 3.6 8.7 - - - +
255C GLU* 2.8 44.4 + - + +
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Residues in contact with THR 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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192C HIS* 3.2 5.9 - - - -
193C HIS* 2.9 49.8 + - + +
198C VAL* 4.9 8.8 - - - +
199C THR* 1.3 73.4 - - - +
201C LEU* 1.3 65.8 + - - +
202C ARG* 3.9 15.8 + - + +
247C THR* 3.8 26.7 - - + -
248C LEU 3.6 3.8 - - - +
249C ALA* 4.5 6.7 - - + +
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Residues in contact with LEU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C VAL* 4.7 1.6 - - + -
191C THR 3.7 3.1 - - - +
192C HIS* 4.0 21.1 - - + -
199C THR* 4.1 9.0 - - + -
200C THR* 1.3 78.3 - - - +
202C ARG* 1.3 59.7 + - - +
217C TRP* 3.6 24.5 - - + -
247C THR* 3.3 5.2 - - - -
248C LEU* 2.8 39.7 + - + +
250C VAL* 4.4 18.2 - - + -
255C GLU* 4.3 11.2 - - + +
258C TYR* 3.7 34.3 - - + +
275C TRP* 4.0 26.5 - - + -
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Residues in contact with ARG 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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189C LYS 3.5 0.9 - - - +
190C VAL* 3.1 5.0 - - - -
191C THR* 2.8 52.0 + - - +
192C HIS* 5.5 0.2 - - - -
200C THR* 3.9 15.1 + - + +
201C LEU* 1.3 75.8 - - - +
203C CYS* 1.3 61.6 + - - +
204C ARG* 4.2 19.1 - - + +
217C TRP* 4.1 2.5 - - - -
245C TRP* 4.2 19.7 - - + +
246C ILE 3.5 8.3 - - - +
247C THR* 3.7 18.7 + - - +
98D ASP* 3.3 32.5 + - - +
99D MET* 3.3 46.8 - - - +
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Residues in contact with CYS 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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188C VAL* 3.7 18.4 - - - -
189C LYS 3.4 3.6 - - - -
190C VAL* 4.2 4.0 - - + +
202C ARG* 1.3 74.7 - - - +
204C ARG* 1.3 63.8 + - - +
215C MET* 4.2 3.0 - - - +
217C TRP* 3.7 12.9 - - + -
245C TRP* 3.0 24.8 - - - +
246C ILE* 3.0 20.7 + - + +
260C CYS* 2.0 53.2 - - + -
262C VAL* 4.2 5.2 - - - -
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Residues in contact with ARG 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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187C LEU 3.3 1.6 - - - +
188C VAL* 3.2 6.9 - - - +
189C LYS* 2.8 40.9 + - + +
191C THR* 5.0 9.1 - - + +
202C ARG* 4.2 20.4 - - + +
203C CYS* 1.3 81.9 - - - +
205C ALA* 1.3 59.6 + - - +
206C LEU* 3.7 19.3 - - + +
215C MET* 4.9 0.2 - - - -
243C GLN* 2.8 28.9 + - - -
244C GLY 3.2 4.7 - - - +
245C TRP* 3.9 17.7 - - + -
11D SER* 2.9 23.2 + - - -
12D ARG 4.0 5.5 + - - -
13D HIS 4.3 0.8 - - - -
14D PRO* 3.5 35.7 - - - +
15D ALA 5.0 0.2 - - - +
97D ARG 5.6 0.4 + - - -
98D ASP 4.3 5.0 + - - -
99D MET* 3.0 32.0 + - - +
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Residues in contact with ALA 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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186C PRO* 3.8 10.8 - - + -
187C LEU 3.5 4.5 - - - -
188C VAL* 4.6 2.7 - - + +
203C CYS 4.3 0.2 + - - -
204C ARG* 1.3 74.3 - - - +
206C LEU* 1.3 58.8 + - - +
208C TYR* 3.7 6.2 - - + -
213C ILE* 3.5 31.4 - - + -
215C MET* 3.9 16.1 - - - -
243C GLN* 3.0 8.8 - - - +
244C GLY 2.8 29.7 + - - +
262C VAL* 4.7 4.9 - - + -
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Residues in contact with LEU 206 (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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185C PRO 4.2 0.3 - - - +
186C PRO* 3.2 3.8 - - - +
187C LEU* 2.8 50.3 + - + +
189C LYS* 4.4 16.4 - - + -
204C ARG* 3.7 39.5 - - + +
205C ALA* 1.3 77.7 - - - +
207C ASN* 1.3 87.7 + - - +
208C TYR 3.1 4.1 + - - -
242C TYR 3.8 0.4 - - - -
243C GLN* 4.1 9.9 - - + +
12D ARG 3.8 18.2 - - - +
13D HIS* 4.8 3.6 - - + -
14D PRO* 3.9 23.6 - - + -
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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