Contacts of the strand formed by residues 169 - 173 (chain A) in PDB entry 1EQB
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 MET 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A VAL* 3.8 18.4 - - + +
106A TYR* 5.0 5.4 - - - -
109A LEU* 3.5 41.5 - - + -
110A LEU* 4.0 28.7 - - + -
115A THR 3.6 2.2 + - - -
116A VAL* 3.5 8.5 - - + +
117A LEU 3.0 22.9 + - - -
167A PRO* 3.2 5.0 - - - +
168A LYS* 1.3 82.4 - - - +
170A ILE* 1.3 75.1 + - - +
171A ILE* 4.2 9.0 - - + -
195A ALA* 4.3 0.2 - - - -
196A TYR* 3.3 17.9 - - + +
198A PHE* 3.8 27.6 - - + -
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Residues in contact with ILE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.5 37.5 - - + +
145A TYR* 4.9 1.6 - - + -
158A LEU* 5.0 2.5 - - + -
162A ALA* 4.1 7.0 - - + -
167A PRO* 4.0 10.8 - - + -
169A MET* 1.3 78.4 - - - +
171A ILE* 1.3 64.9 + - - +
186A MET* 3.9 28.5 - - + +
189A ILE* 3.9 26.9 - - + -
190A ALA* 4.2 18.2 - - + +
193A ILE* 4.4 2.9 - - + -
195A ALA* 4.4 4.7 - - + -
196A TYR 2.7 13.7 + - - +
197A LEU* 3.5 11.7 - - + +
198A PHE* 2.9 25.8 + - - +
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Residues in contact with ILE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A TYR* 3.1 33.0 - - + +
116A VAL* 3.6 28.3 - - + -
117A LEU 2.7 13.1 + - - +
118A GLY* 4.1 6.6 - - - -
119A MET* 4.4 1.7 + - - +
129A HIS* 4.0 41.5 - - + +
145A TYR* 2.6 34.5 + - - -
169A MET* 4.4 3.6 - - - -
170A ILE* 1.3 74.3 - - - +
172A GLY* 1.3 63.1 + - - +
186A MET* 3.9 3.5 - - - +
198A PHE* 3.2 30.5 - - + +
200A ASP* 5.1 0.9 - - + -
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Residues in contact with GLY 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A TYR* 3.8 6.1 - - - -
170A ILE 4.0 1.2 + - - -
171A ILE* 1.3 78.5 - - - +
173A GLY* 1.3 57.6 + - - -
181A VAL* 5.6 0.4 - - - -
183A TRP* 4.2 7.4 - - - -
186A MET* 3.9 21.0 - - - +
197A LEU* 4.6 0.6 - - - +
198A PHE 2.8 9.7 + - - +
199A VAL* 3.0 14.0 - - - +
200A ASP 2.8 24.9 + - - -
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Residues in contact with GLY 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A MET* 3.8 17.5 - - - +
129A HIS* 3.9 16.3 + - - -
145A TYR* 4.5 2.5 + - - -
172A GLY* 1.3 75.2 - - - -
174A PHE* 1.3 77.9 + - - +
181A VAL* 5.5 2.0 - - - +
183A TRP* 4.3 9.8 - - - -
200A ASP 3.3 16.2 - - - -
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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