Contacts of the strand formed by residues 161 - 166 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84U HIS* 3.3 12.1 - - + -
85U LEU* 4.6 1.1 - - - -
86U ILE* 4.9 1.1 - - - -
145U GLY* 3.6 26.2 - - - +
148U ILE* 3.7 30.1 - - + -
149U ALA* 4.2 8.7 - - + +
152U CYS* 4.8 0.4 - - - -
160U VAL* 1.3 78.5 - - - +
162U LEU* 1.3 70.9 + - - +
163U THR* 3.8 11.4 + - - +
188U PRO 3.1 11.4 + - - +
189U CYS* 3.9 0.6 - - - -
190U ILE* 3.0 30.0 + - - +
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Residues in contact with LEU 162 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75U LEU* 3.7 39.5 - - + -
79U ILE* 4.0 33.4 - - + -
83U ASP* 5.5 0.2 - - + -
84U HIS 2.7 17.4 + - - +
85U LEU* 3.3 18.8 - - + +
86U ILE* 2.9 29.8 + - - +
160U VAL* 4.2 7.2 - - + -
161U CYS* 1.3 75.4 - - - +
163U THR* 1.3 60.1 + - - +
164U LEU* 4.0 1.6 - - - -
190U ILE* 3.6 29.4 - - + -
192U ILE* 3.6 18.4 - - + -
237U THR* 4.7 4.7 - - + +
253U MET* 5.7 0.2 - - + -
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Residues in contact with THR 163 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86U ILE* 3.7 6.3 - - + -
141U GLN 3.6 8.1 - - - +
142U VAL* 3.5 48.5 - - + +
145U GLY* 3.3 23.8 - - - -
161U CYS* 3.8 3.3 - - - -
162U LEU* 1.3 73.5 - - - +
164U LEU* 1.3 58.7 + - - +
165U TYR* 4.2 2.1 - - - -
189U CYS* 3.6 15.0 - - - -
190U ILE 2.8 12.8 + - - -
191U PHE* 3.4 8.0 - - + -
192U ILE 2.6 29.8 + - - +
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Residues in contact with LEU 164 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75U LEU* 4.2 7.2 - - + -
85U LEU* 4.1 14.6 - - + -
86U ILE* 3.1 15.2 + - - +
87U THR* 3.6 19.5 - - - +
88U ALA 3.9 1.6 + - - -
94U PHE* 3.3 35.2 - - + -
141U GLN* 3.1 24.9 + - - +
162U LEU 4.0 8.3 - - - +
163U THR* 1.3 78.9 - - - +
165U TYR* 1.3 62.8 + - - +
192U ILE* 3.1 38.4 - - + +
194U GLU* 3.6 23.3 - - + +
255U LEU* 5.6 1.6 - - + -
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Residues in contact with TYR 165 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88U ALA* 5.3 2.0 - - - -
141U GLN* 3.6 16.8 - - - +
142U VAL* 3.3 28.5 - - + -
163U THR 4.2 3.6 - - - -
164U LEU* 1.3 77.6 - - - +
166U GLY* 1.3 72.6 + - - +
169U ALA* 4.0 10.3 - - + -
170U ALA* 4.4 14.1 - - + -
175U ILE* 4.1 17.5 - - + -
179U TYR* 2.6 31.3 + - - -
191U PHE* 4.2 11.5 - + + +
192U ILE 2.8 19.4 + - - -
193U CYS* 3.3 32.3 + - + +
194U GLU* 3.0 27.2 + - - -
213U TYR* 6.0 0.4 - + + -
252U LEU* 3.9 13.3 - - - +
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Residues in contact with GLY 166 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88U ALA* 5.4 5.9 - - - +
141U GLN* 5.0 0.8 - - - +
165U TYR* 1.3 82.1 - - - +
167U ASP* 1.3 67.8 + - - -
168U GLY 3.2 3.4 - - - -
169U ALA* 3.0 21.1 + - - +
170U ALA 3.5 3.1 + - - -
193U CYS* 4.4 0.4 - - - -
194U GLU* 3.4 17.1 + - - +
196U ASN* 6.1 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