Contacts of the strand formed by residues 174 - 178 (chain A) in PDB entry 1P4J
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 TRP 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ILE* 3.2 7.2 - - - -
171A CYS* 2.8 39.6 + - - +
172A GLY* 3.2 22.8 + - - -
173A GLY* 1.3 80.0 - - - +
175A GLN* 1.3 67.9 + - - +
176A MET* 4.2 5.7 - - - +
617A LYS* 4.3 16.4 - - + -
618A MET* 3.5 36.6 - - + -
620A ILE* 5.2 0.7 - - - -
621A LYS* 3.6 43.1 - - + +
754A GLN* 5.0 5.7 + - - +
757A LEU* 3.9 19.7 - - + -
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Residues in contact with GLN 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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166A PHE* 3.4 15.4 - - - -
168A GLN* 2.8 37.1 + - + +
169A LYS 3.5 4.3 - - - -
170A ILE* 4.1 5.3 - - + +
174A TRP* 1.3 77.4 - - - +
176A MET* 1.3 73.9 + - - +
177A GLU* 2.8 28.3 + - + +
608A LYS* 3.9 0.3 - - - -
609A ALA* 2.9 41.4 + - - -
611A PRO 4.7 0.2 - - - -
617A LYS* 3.7 25.3 + - + +
620A ILE* 3.4 21.3 - - + +
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Residues in contact with MET 176 (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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168A GLN* 3.7 4.9 - - - -
169A LYS* 2.7 45.9 + - + +
171A CYS* 3.5 36.6 - - + -
174A TRP* 4.2 7.0 - - - +
175A GLN* 1.3 85.9 - - - +
177A GLU* 1.3 66.4 + - - +
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Residues in contact with GLU 177 (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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166A PHE* 3.6 34.8 - - + -
167A ASN 3.8 3.8 - - - -
175A GLN* 2.8 22.2 + - - +
176A MET* 1.3 77.6 - - - +
178A GLU* 1.3 64.2 + - - +
611A PRO* 4.0 20.2 - - + +
617A LYS* 2.7 33.8 + - - -
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Residues in contact with GLU 178 (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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166A PHE* 3.6 6.3 - - - +
167A ASN* 2.9 56.6 + - + +
169A LYS* 2.7 47.1 + - + +
177A GLU* 1.3 77.5 - - - +
179A ALA* 1.3 66.7 + - - +
180A ASP 3.4 0.3 + - - -
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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