Contacts of the strand formed by residues 189 - 195 (chain S) in PDB entry 3EXG
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 CYS 189 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146S ALA* 4.3 12.8 - - - -
149S ALA* 3.6 16.4 - - + -
161S CYS 3.5 3.8 - - - -
163S THR* 3.6 22.7 - - - -
182S ALA* 4.9 0.9 - - + -
187S LEU* 2.7 17.3 + - + +
188S PRO* 1.3 74.1 - - - +
190S ILE* 1.3 64.6 + - - +
191S PHE* 3.5 41.2 + - + -
244S CYS* 3.6 4.4 - - - -
250S PRO* 3.3 22.8 - - + +
251S ILE 3.3 4.3 + - - -
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Residues in contact with ILE 190 (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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79S ILE* 5.7 0.4 - - + -
160S VAL* 4.1 9.4 - - + -
161S CYS 2.7 15.2 + - - +
162S LEU* 3.6 24.3 - - + -
163S THR 2.9 26.4 + - - -
189S CYS* 1.3 72.1 - - - +
191S PHE* 1.3 62.1 + - - +
192S ILE* 3.4 23.6 + - + +
237S THR* 5.1 2.5 - - + +
240S ALA* 4.1 9.0 - - + -
241S ALA* 3.8 34.3 - - + +
244S CYS* 3.5 20.9 - - + -
251S ILE* 3.5 17.5 - - + +
253S MET* 4.6 8.5 - - + -
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Residues in contact with PHE 191 (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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142S VAL* 3.5 36.6 - - + -
146S ALA* 4.8 2.2 - - + -
163S THR* 3.5 7.6 - - + -
165S TYR* 4.0 12.6 - + + -
178S ALA* 4.0 13.5 - - + -
179S TYR* 3.8 34.3 - + + -
182S ALA* 3.7 28.5 - - + -
189S CYS* 3.5 28.7 - - - -
190S ILE* 1.3 69.4 - - - +
192S ILE* 1.3 60.4 + - - +
193S CYS 3.8 1.5 + - - -
220S ILE* 4.4 1.6 - - + -
250S PRO* 4.1 13.5 - - + -
251S ILE 2.9 11.5 + - - -
252S LEU* 3.4 18.2 - - + +
253S MET 2.8 26.9 + - - +
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Residues in contact with ILE 192 (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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75S LEU* 4.1 7.9 - - + -
162S LEU* 3.8 38.4 - - + -
163S THR 2.7 11.0 + - - +
164S LEU* 3.0 26.9 - - + +
165S TYR* 2.8 33.0 + - - +
190S ILE* 3.8 17.3 - - + +
191S PHE* 1.3 77.5 - - - +
193S CYS* 1.3 59.0 + - - +
194S GLU* 3.6 2.0 + - + -
237S THR* 6.3 0.4 - - + -
253S MET* 3.3 32.3 - - + +
255S LEU* 4.3 21.3 - - + -
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Residues in contact with CYS 193 (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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165S TYR* 3.2 38.5 - - + +
167S ASP* 3.8 20.6 - - - -
170S ALA* 5.1 0.2 - - - -
191S PHE 3.8 2.4 + - - -
192S ILE* 1.3 70.5 - - - +
194S GLU* 1.3 61.2 + - - +
195S ASN* 3.0 12.0 + - - -
213S TYR* 3.9 35.4 - - + -
252S LEU* 6.1 2.0 - - + +
253S MET 3.0 10.4 + - - +
254S GLU* 3.5 5.8 - - + +
255S LEU 2.9 27.6 + - - -
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Residues in contact with GLU 194 (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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68S GLN* 3.4 23.7 - - - +
71S CYS* 3.4 30.5 - - - +
87S THR* 5.0 4.2 + - - -
90S ARG* 5.2 11.3 - - - +
94S PHE* 4.3 11.3 - - - -
164S LEU* 4.0 35.6 - - + +
165S TYR 2.8 12.4 + - - +
166S GLY* 3.4 6.9 - - - -
167S ASP* 3.1 20.7 + - - +
192S ILE* 3.6 6.0 + - + -
193S CYS* 1.3 68.5 - - - +
195S ASN* 1.3 60.6 + - - +
196S ASN* 3.4 7.6 + - - +
255S LEU* 3.9 10.0 - - + +
257S THR* 4.7 3.1 - - + -
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Residues in contact with ASN 195 (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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167S ASP* 3.6 15.4 - - + +
193S CYS* 3.0 8.3 + - - +
194S GLU* 1.3 71.7 - - - +
196S ASN* 1.3 56.1 + - - +
197S ARG* 2.9 29.9 + - - +
211S THR 5.3 1.0 + - - -
213S TYR* 3.8 23.2 - - + -
254S GLU* 3.0 35.9 + - + +
255S LEU 3.0 11.4 + - - +
256S GLN* 3.5 15.7 - - - +
257S THR* 3.0 21.2 + - - +
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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