Contacts of the strand formed by residues 161 - 166 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84O HIS 3.2 9.0 - - - -
85O LEU* 4.9 0.2 - - - -
86O ILE* 4.8 1.8 - - - -
145O GLY* 3.5 22.0 - - - -
148O ILE* 3.8 25.8 - - + -
149O ALA* 3.8 26.9 - - + +
152O CYS* 5.0 0.4 - - - -
160O VAL* 1.3 77.8 - - - +
162O LEU* 1.3 78.3 + - - +
163O THR* 3.7 8.1 + - - -
188O PRO 3.0 9.1 + - - -
189O CYS* 3.6 2.9 - - - -
190O ILE* 3.1 23.8 + - - +
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Residues in contact with LEU 162 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75O LEU* 3.8 32.5 - - + +
79O ILE* 3.8 38.1 - - + -
83O ASP* 5.4 0.4 - - + -
84O HIS 2.8 15.6 + - - +
85O LEU* 3.5 22.7 - - + -
86O ILE 3.0 27.4 + - - +
160O VAL* 4.3 8.1 - - + +
161O CYS* 1.3 85.3 - - - +
163O THR* 1.3 59.3 + - - +
164O LEU* 3.8 2.5 - - + -
190O ILE* 3.5 24.2 - - + -
192O ILE* 4.1 16.4 - - + -
237O THR* 4.5 4.7 - - + -
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Residues in contact with THR 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O ILE* 3.8 7.4 - - + -
141O GLN 3.7 9.9 - - - +
142O VAL* 3.6 44.6 - - + +
145O GLY* 3.2 28.2 - - - -
161O CYS* 3.7 2.9 - - - -
162O LEU* 1.3 73.4 + - - +
164O LEU* 1.3 60.1 + - - +
165O TYR* 3.9 3.5 - - - -
189O CYS* 3.6 9.1 - - - -
190O ILE 3.1 10.7 + - - -
191O PHE* 3.6 11.6 - - + -
192O ILE* 2.9 21.8 + - - +
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Residues in contact with LEU 164 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71O CYS* 5.9 0.2 - - + -
75O LEU* 4.3 8.3 - - + -
85O LEU* 3.8 32.5 - - + -
86O ILE 3.2 16.7 + - - +
87O THR* 3.9 17.8 - - - +
88O ALA 4.1 0.2 + - - -
94O PHE* 3.2 33.0 - - + -
141O GLN* 3.4 22.7 + - - +
162O LEU* 4.6 3.8 - - + +
163O THR* 1.3 74.4 - - - +
165O TYR* 1.3 65.1 + - - +
192O ILE* 3.1 25.8 - - + +
194O GLU* 3.6 26.2 - - + +
255O LEU* 5.6 1.8 - - + -
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Residues in contact with TYR 165 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87O THR* 5.6 0.2 - - - -
88O ALA* 5.1 3.1 - - - +
139O GLY* 5.8 0.2 - - - -
141O GLN* 3.4 20.2 - - - +
142O VAL* 3.8 23.3 - - + -
163O THR 3.9 5.2 - - - -
164O LEU* 1.3 79.6 - - - +
166O GLY* 1.3 66.4 + - - +
169O ALA* 4.5 5.4 - - + -
170O ALA* 4.0 20.4 - - + +
175O ILE* 3.8 21.8 - - + -
179O TYR* 2.4 29.9 + - - -
191O PHE* 4.5 9.9 - + + -
192O ILE 2.8 25.8 + - - -
193O CYS* 3.2 27.2 - - + +
194O GLU* 2.8 33.3 + - - -
213O TYR* 5.0 1.2 + - - +
252O LEU* 3.5 15.2 - - - +
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Residues in contact with GLY 166 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88O ALA* 5.4 3.8 - - - +
141O GLN* 4.9 1.0 - - - +
165O TYR* 1.3 92.9 - - - +
167O ASP* 1.3 67.4 + - - +
168O GLY 3.0 4.0 - - - -
169O ALA* 3.1 17.8 + - - +
170O ALA 3.6 1.2 + - - -
193O CYS* 4.2 1.1 - - - -
194O GLU* 3.8 11.0 + - - -
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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