Contacts of the strand formed by residues 161 - 166 (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 161 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84S HIS* 3.3 12.8 - - + +
85S LEU 4.9 0.4 - - - -
86S ILE* 5.0 1.8 - - - -
145S GLY* 3.7 23.3 - - - -
148S ILE* 3.8 26.2 - - + -
149S ALA* 3.9 20.2 - - + +
152S CYS* 4.5 0.9 - - - -
160S VAL* 1.3 79.2 - - - +
162S LEU* 1.3 66.8 + - - +
163S THR* 3.8 10.1 + - - -
188S PRO 2.9 13.3 + - - +
189S CYS* 3.5 1.6 - - - -
190S ILE* 2.7 32.0 + - - +
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Residues in contact with LEU 162 (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* 3.9 19.3 - - + -
79S ILE* 3.8 37.2 - - + -
83S ASP* 5.4 0.4 - - + -
84S HIS 2.8 15.4 + - - +
85S LEU* 3.4 27.2 - - + -
86S ILE* 3.0 27.2 + - - +
160S VAL* 4.2 7.6 - - + -
161S CYS* 1.3 77.0 - - - +
163S THR* 1.3 60.8 + - - +
164S LEU* 3.9 4.2 - - + +
190S ILE* 3.6 24.9 - - + -
192S ILE* 3.8 23.8 - - + -
237S THR* 5.1 2.2 - - + -
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Residues in contact with THR 163 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86S ILE* 3.7 7.0 - - + -
141S GLN 3.8 8.7 - - - +
142S VAL* 3.6 48.5 - - + +
145S GLY* 3.4 20.0 - - - -
161S CYS* 3.8 4.2 - - - -
162S LEU* 1.3 77.4 + - - +
164S LEU* 1.3 57.2 + - - +
165S TYR* 4.2 2.6 - - - -
189S CYS* 3.6 19.5 - - - -
190S ILE 2.9 10.5 + - - -
191S PHE* 3.5 5.5 - - + -
192S ILE* 2.7 28.8 + - - +
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Residues in contact with LEU 164 (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* 4.0 11.0 - - + -
85S LEU* 3.4 29.2 - - + -
86S ILE 3.1 14.1 + - - +
87S THR* 3.6 19.6 - - - +
94S PHE* 3.3 36.8 - - + -
141S GLN* 3.3 23.6 + - - +
142S VAL* 4.3 0.7 - - - +
162S LEU* 3.9 8.5 - - + +
163S THR* 1.3 78.3 - - - +
165S TYR* 1.3 66.1 + - - +
192S ILE* 3.0 23.1 - - + +
194S GLU* 4.0 22.7 - - + -
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Residues in contact with TYR 165 (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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87S THR* 5.7 0.2 - - - -
88S ALA* 5.4 1.8 - - - -
141S GLN* 3.7 17.0 - - - +
142S VAL* 3.6 25.1 - - + -
163S THR 4.2 2.9 - - - -
164S LEU* 1.3 78.6 - - - +
166S GLY* 1.3 67.9 + - - +
169S ALA* 4.1 8.3 - - + -
170S ALA* 4.4 13.5 - - + -
175S ILE* 3.9 20.2 - - + -
179S TYR* 2.6 28.3 + - - -
191S PHE* 4.0 24.2 - + + +
192S ILE 2.8 14.7 + - - -
193S CYS* 3.2 37.2 + - + +
194S GLU* 2.8 24.7 + - - -
213S TYR* 4.9 2.8 + - + +
252S LEU* 4.2 13.0 - - - +
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Residues in contact with GLY 166 (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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88S ALA* 5.5 4.6 - - - +
141S GLN* 5.0 0.8 - - - +
165S TYR* 1.3 79.8 - - - +
167S ASP* 1.3 67.4 + - - -
168S GLY 2.8 7.4 - - - -
169S ALA* 2.7 22.6 + - - +
170S ALA* 3.5 6.1 + - - +
193S CYS* 4.1 1.6 - - - -
194S GLU* 3.4 11.4 - - - -
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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