Contacts of the strand formed by residues 182 - 187 (chain S) in PDB entry 6NZO
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 VAL 182 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180S ALA* 3.9 3.2 + - + +
181S LYS* 1.3 80.6 + - - +
183S SER* 1.3 70.2 + - - +
194S LEU* 4.0 42.0 - - + -
195S ARG 3.0 13.0 - - - +
196S ALA* 4.6 0.7 - - + -
197S ASP* 3.0 5.6 - - - +
200S LEU* 5.6 1.6 - - + -
206S ILE* 4.7 17.0 - - + -
207S TYR* 5.1 16.6 - - + -
253S LEU* 5.1 14.8 - - + +
292S LEU* 4.4 16.6 - - + -
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Residues in contact with SER 183 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89S PRO* 4.0 19.0 - - - +
90S GLN 5.7 0.2 - - - -
182S VAL* 1.3 71.8 + - - +
184S VAL* 1.3 67.2 + - - +
193S GLY 2.9 3.8 - - - +
194S LEU* 3.2 6.0 - - - -
195S ARG* 2.9 40.2 + - - +
197S ASP* 2.4 32.7 + - - -
253S LEU* 6.0 2.0 - - - -
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Residues in contact with VAL 184 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89S PRO* 3.3 4.8 - - - +
90S GLN* 2.5 62.9 + - + +
91S LEU 3.7 13.0 - - - +
102S ALA* 5.2 0.7 - - - -
183S SER* 1.3 78.7 - - - +
185S ILE* 1.3 57.4 + - - +
186S LYS 4.0 0.3 + - - -
192S TYR* 4.3 17.0 - - + -
193S GLY 3.5 3.4 - - - +
194S LEU* 4.7 0.7 - - + -
195S ARG* 4.8 0.4 - - - -
253S LEU* 4.1 13.5 - - + -
256S PHE* 3.6 52.9 - - + -
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Residues in contact with ILE 185 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83S LEU* 3.6 34.3 - - + +
84S PRO 3.3 23.3 - - - +
88S PRO 4.3 17.5 - - - +
89S PRO* 5.0 0.2 - - - -
183S SER 3.6 1.0 + - - -
184S VAL* 1.3 75.6 - - - +
186S LYS* 1.3 74.4 + - - +
187S THR* 3.7 7.3 + - + -
191S GLY 3.7 0.2 - - - +
192S TYR* 3.3 7.8 - - - +
193S GLY* 2.9 53.0 + - - +
195S ARG* 3.5 33.7 - - + +
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Residues in contact with LYS 186 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88S PRO 4.9 5.1 + - - +
90S GLN* 5.3 0.6 - - + +
101S GLU* 3.8 35.0 + - + +
184S VAL 4.0 2.0 + - - -
185S ILE* 1.3 83.9 - - + +
187S THR* 1.3 91.0 + - - +
188S GLU* 4.4 8.1 + - - +
191S GLY* 3.5 17.1 + - - +
192S TYR* 3.6 29.8 + - + -
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Residues in contact with THR 187 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83S LEU* 4.8 6.7 - - + -
185S ILE* 3.7 16.3 + - + -
186S LYS* 1.3 92.3 + - - +
188S GLU* 1.3 66.4 + - - +
189S LYS 3.2 0.2 - - - -
190S LYS* 3.2 38.6 - - - +
191S GLY 2.7 57.5 + - - +
192S TYR* 3.9 1.6 + - - -
193S GLY 4.7 0.3 + - - -
291S GLU* 4.1 9.5 + - - +
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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