Contacts of the strand formed by residues 161 - 166 (chain C) in PDB entry 3EXF
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C HIS* 3.3 9.6 - - + -
85C LEU 4.6 0.7 - - - -
86C ILE* 4.4 4.7 - - - -
145C GLY* 3.4 20.9 - - - -
148C ILE* 3.6 24.0 - - + +
149C ALA* 3.8 28.9 - - + +
152C CYS* 4.9 0.6 - - - -
160C VAL* 1.3 73.8 - - - +
162C LEU* 1.3 66.4 + - - +
163C THR* 3.7 13.0 + - - +
188C PRO 3.0 7.1 + - - -
189C CYS* 3.4 3.3 - - - +
190C ILE* 2.8 33.1 + - - +
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Residues in contact with LEU 162 (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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75C LEU* 4.0 23.8 - - + -
79C ILE* 3.9 34.3 - - + -
84C HIS 2.8 19.3 + - - +
85C LEU* 4.2 11.2 - - + -
86C ILE* 2.9 31.5 + - - +
160C VAL* 4.2 7.0 - - + +
161C CYS* 1.3 71.9 - - - +
163C THR* 1.3 61.7 + - - +
164C LEU* 3.8 9.0 - - + +
190C ILE* 3.6 30.1 - - + -
192C ILE* 3.5 26.0 - - + -
237C THR* 4.5 7.0 - - + -
253C MET* 5.7 0.9 - - + -
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Residues in contact with THR 163 (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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86C ILE* 3.6 4.9 - - + -
141C GLN* 3.6 10.1 - - + +
142C VAL* 3.5 45.1 - - + +
145C GLY* 3.4 24.9 - - - -
161C CYS* 3.7 4.3 - - - -
162C LEU* 1.3 74.3 + - - +
164C LEU* 1.3 61.4 - - - +
165C TYR* 3.6 5.4 - - - -
189C CYS* 4.1 5.5 - - - -
190C ILE 3.0 13.3 + - - -
191C PHE* 3.8 14.4 - - + -
192C ILE* 3.1 21.6 + - - +
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Residues in contact with LEU 164 (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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71C CYS* 6.0 0.4 - - + -
75C LEU* 3.8 15.0 - - + -
85C LEU* 4.1 19.7 - - + -
86C ILE 3.0 17.2 + - - +
87C THR* 3.1 23.1 + - - +
88C ALA 4.0 0.2 + - - -
94C PHE* 3.4 31.9 - - + -
141C GLN* 2.7 32.9 + - - +
162C LEU* 3.8 22.0 - - + +
163C THR* 1.3 73.6 - - - +
165C TYR* 1.3 54.3 + - - +
192C ILE* 3.6 23.6 - - + +
194C GLU* 4.4 20.0 - - + +
255C LEU* 5.7 1.3 - - + -
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Residues in contact with TYR 165 (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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88C ALA* 5.6 2.9 - - - -
141C GLN* 3.3 18.8 - - - +
142C VAL* 3.7 19.3 - - + -
163C THR 3.6 8.7 - - - -
164C LEU* 1.3 73.5 - - - +
166C GLY* 1.3 63.8 + - - +
169C ALA* 4.0 9.4 - - + -
170C ALA* 3.9 23.1 - - + -
175C ILE* 3.8 19.5 - - + -
179C TYR* 2.5 30.1 + - - -
191C PHE* 4.3 9.0 - + + -
192C ILE 2.9 28.6 + - - +
193C CYS* 3.3 13.4 - - + +
194C GLU* 2.5 39.9 + - - +
213C TYR* 5.4 0.6 + - + -
252C LEU* 3.6 19.8 - - - +
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Residues in contact with GLY 166 (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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88C ALA* 6.0 1.6 - - - +
165C TYR* 1.3 85.1 - - - +
167C ASP* 1.3 69.6 + - - +
168C GLY 3.2 2.9 - - - -
169C ALA* 3.2 3.0 + - - +
170C ALA* 3.2 14.9 + - - +
193C CYS* 4.1 3.8 - - - -
194C GLU* 3.3 15.5 - - - -
1006C TPP 3.4 22.3 + - - -
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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