Contacts of the strand formed by residues 171 - 175 (chain A) in PDB entry 3E6D
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 THR 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A ARG* 3.4 4.2 - - - +
168A VAL* 2.8 47.1 + - + +
170A ASP* 1.3 87.3 - - + +
172A TYR* 1.3 80.7 + - - +
173A GLU* 4.5 2.8 + - - +
215A ILE* 4.4 11.6 - - + +
216A VAL 3.3 14.6 - - - -
217A TYR* 4.3 20.6 - - + -
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Residues in contact with TYR 172 (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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161A CYS* 3.5 33.0 - - - -
162A SER* 6.0 1.6 - - - -
165A GLY* 4.0 19.3 - - - -
166A LYS 3.5 5.2 - - - +
167A ARG* 3.9 38.0 - - + +
170A ASP 5.6 0.7 - - - -
171A THR* 1.3 93.1 - - - +
173A GLU* 1.3 62.7 + - - +
214A ILE 3.6 0.9 - - - +
215A ILE* 3.4 4.9 - - - +
216A VAL* 2.8 38.8 + - + +
219A LEU* 4.0 32.1 - - + +
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Residues in contact with GLU 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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164A GLN 4.2 1.2 - - - +
165A GLY* 3.4 1.4 - - - -
166A LYS* 2.9 40.0 + - + +
168A VAL* 4.0 29.5 - - + +
171A THR* 4.5 5.6 + - - +
172A TYR* 1.3 78.3 - - - +
174A ILE* 1.3 62.0 + - - +
175A THR* 4.2 3.7 + - - +
213A LYS* 3.2 28.5 - - + +
214A ILE 3.4 3.1 - - - +
215A ILE* 4.5 19.3 - - + +
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Residues in contact with ILE 174 (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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157A PHE* 4.6 2.7 - - + +
160A LEU* 4.0 8.1 - - + +
161A CYS* 3.5 39.9 - - + +
164A GLN* 3.9 24.9 - - + +
165A GLY* 3.8 14.6 - - - -
172A TYR 5.2 0.4 - - - +
173A GLU* 1.3 78.1 - - - +
175A THR* 1.3 64.1 + - - +
176A MET* 3.5 31.0 + - + -
207A LEU* 6.3 0.2 - - + -
213A LYS* 3.7 3.5 - - - +
214A ILE* 2.9 61.4 + - + +
216A VAL* 4.6 4.3 - - + -
164B GLN* 5.3 0.4 - - - +
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Residues in contact with THR 175 (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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164A GLN 5.4 1.0 + - - -
173A GLU* 4.2 3.5 + - - +
174A ILE* 1.3 71.7 + - - +
176A MET* 1.3 68.5 + - - +
212A ASN* 3.9 11.4 - - + +
213A LYS* 4.8 11.8 - - + +
163B SER 5.2 0.5 - - - +
164B GLN* 3.6 12.8 + - - +
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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