Contacts of the strand formed by residues 161 - 166 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84M HIS* 3.4 8.3 - - - -
86M ILE* 4.6 1.3 - - - -
145M GLY* 3.5 24.7 - - - -
148M ILE* 3.9 25.8 - - + -
149M ALA* 4.0 19.7 - - + +
152M CYS* 4.7 0.2 - - - -
160M VAL* 1.3 78.9 - - - +
162M LEU* 1.3 66.3 + - - +
163M THR* 3.7 12.3 + - - -
188M PRO 3.0 11.6 + - - +
189M CYS* 3.6 0.6 - - - -
190M ILE* 2.8 35.5 + - - +
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Residues in contact with LEU 162 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75M LEU* 3.9 19.1 - - + -
79M ILE* 3.9 32.5 - - + -
83M ASP* 5.5 0.2 - - + -
84M HIS 2.8 12.4 + - - +
85M LEU* 3.4 30.9 - - + +
86M ILE* 3.0 28.8 + - - +
160M VAL* 3.9 11.7 - - + -
161M CYS* 1.3 76.0 - - - +
163M THR* 1.3 59.3 + - - +
164M LEU* 4.1 1.8 - - + -
190M ILE* 3.6 29.4 - - + -
192M ILE* 3.6 27.6 - - + -
237M THR* 4.7 4.7 - - + -
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Residues in contact with THR 163 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M ILE* 3.7 5.6 - - + -
141M GLN* 3.6 8.1 - - + +
142M VAL* 3.5 48.9 - - + +
145M GLY* 3.3 26.7 + - - -
161M CYS* 3.7 2.6 - - - -
162M LEU* 1.3 70.7 - - - +
164M LEU* 1.3 56.6 + - - +
165M TYR* 4.1 2.6 - - - -
189M CYS* 3.6 8.1 - - - -
190M ILE 2.9 12.8 + - - -
191M PHE* 3.5 12.2 - - + -
192M ILE 2.7 29.3 + - - +
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Residues in contact with LEU 164 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75M LEU* 4.3 7.2 - - + -
85M LEU* 4.1 25.4 - - + -
86M ILE 2.9 17.8 + - - +
87M THR* 3.5 23.4 + - - +
88M ALA 3.8 2.1 + - - -
94M PHE* 3.3 35.9 - - + -
141M GLN* 2.8 20.5 + - - -
162M LEU* 4.1 4.3 - - + +
163M THR* 1.3 77.2 - - - +
165M TYR* 1.3 61.0 + - - +
192M ILE* 3.1 33.9 - - + +
194M GLU* 3.7 24.0 - - + -
255M LEU* 5.7 0.2 - - + -
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Residues in contact with TYR 165 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88M ALA* 5.3 2.5 - - - -
141M GLN* 3.6 16.4 - - - +
142M VAL* 3.4 28.9 - - + -
163M THR 4.1 4.5 - - - -
164M LEU* 1.3 76.5 - - - +
166M GLY* 1.3 64.9 + - - +
169M ALA* 4.1 10.5 - - + -
170M ALA* 4.3 10.8 - - + -
175M ILE* 3.9 17.9 - - + -
179M TYR* 2.6 31.9 + + - -
191M PHE* 4.3 11.7 - + + +
192M ILE 2.9 20.6 + - - +
193M CYS* 3.4 27.7 + - + +
194M GLU* 2.8 35.7 + - - +
213M TYR* 6.0 0.4 - + + -
252M LEU* 3.4 19.1 - - - +
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Residues in contact with GLY 166 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88M ALA* 5.5 4.2 - - - +
165M TYR* 1.3 82.8 - - - +
167M ASP* 1.3 72.6 + - - +
168M GLY 3.3 2.5 - - - -
169M ALA* 3.1 19.0 + - - +
170M ALA* 3.5 4.3 + - - +
193M CYS* 4.1 2.5 - - - -
194M GLU* 3.4 13.2 - - - -
196M ASN* 4.8 1.1 - - - -
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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