Contacts of the strand formed by residues 168 - 173 (chain A) in PDB entry 1DY7
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 LEU 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A TRP* 4.1 26.0 - - + -
164A ASP 3.3 9.6 + - - +
165A LEU* 3.1 22.9 + - + +
167A ASN* 1.3 79.9 - - - +
169A PHE* 1.3 63.1 + - - +
181A LEU* 4.1 21.5 - - + -
182A ILE 3.5 26.2 - - - +
183A ASP* 4.1 5.6 - - + +
184A GLY 4.4 0.4 - - - +
190A LYS* 4.1 16.6 - - + -
225A LEU* 4.2 21.5 - - + -
558A ASN* 3.4 3.3 - - - -
559A VAL* 2.9 36.5 + - + +
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Residues in contact with PHE 169 (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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167A ASN 3.6 13.0 - - - -
168A LEU* 1.3 77.0 - - - +
170A SER* 1.3 59.2 + - - +
171A VAL* 3.8 8.2 + - + +
180A ALA 3.3 4.5 - - - +
181A LEU* 3.4 3.4 - - - -
182A ILE* 2.9 36.2 + - + +
184A GLY* 3.8 7.6 - - - -
509A GLU* 3.7 31.2 - - + -
510A PHE 3.6 17.3 - - - -
511A ASN* 3.6 13.9 - - + -
518A TRP* 3.4 72.5 - + + -
556A LYS* 4.4 9.2 - - + -
557A PHE 3.4 3.4 - - - -
558A ASN* 3.7 17.0 - - + -
559A VAL* 5.7 0.2 - - - -
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Residues in contact with SER 170 (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 LEU 4.2 0.2 - - - -
169A PHE* 1.3 71.6 - - - +
171A VAL* 1.3 60.0 + - - +
179A ILE* 3.8 21.8 - - - +
180A ALA 3.6 3.8 - - - -
181A LEU* 4.0 11.2 - - - -
202A SER* 2.8 31.9 + - - -
204A LEU* 5.6 1.6 - - - -
211A LEU* 3.8 11.9 - - - +
555A GLY 3.8 1.4 - - - +
556A LYS* 3.4 2.3 - - - -
557A PHE* 2.8 43.0 + - - -
559A VAL* 5.5 3.7 - - - +
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Residues in contact with VAL 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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169A PHE* 4.2 14.4 - - + +
170A SER* 1.3 74.8 + - - +
172A THR* 1.3 71.0 + - - +
173A LEU* 3.5 7.4 + - + +
179A ILE* 3.1 7.9 - - - -
180A ALA* 2.8 44.9 + - + +
182A ILE* 3.9 24.0 - - + -
518A TRP* 4.8 0.4 - - + -
531A LEU* 4.1 13.9 - - + -
550A LEU* 4.7 1.8 - - + -
553A PRO* 4.3 16.4 - - + -
554A THR 4.9 0.2 - - - +
555A GLY 3.4 8.3 - - - +
556A LYS* 3.9 25.6 - - + -
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Residues in contact with THR 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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170A SER 4.1 0.8 + - - -
171A VAL* 1.3 73.2 - - - +
173A LEU* 1.3 63.2 + - - +
174A ARG* 3.6 16.2 - - + +
178A GLN 4.1 3.8 - - - +
179A ILE* 4.2 4.8 - - - +
199A VAL* 3.2 50.5 + - + +
200A HIS 4.7 4.3 + - - -
202A SER* 5.0 3.8 + - - -
552A THR 3.6 0.2 - - - +
553A PRO* 3.2 6.9 - - - +
554A THR* 3.1 43.6 + - - +
555A GLY* 2.8 20.6 + - - -
557A PHE* 5.1 2.6 - - - -
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Residues in contact with LEU 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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171A VAL* 3.9 13.5 - - + +
172A THR* 1.3 77.9 - - - +
174A ARG* 1.3 67.0 + - - +
175A ASP 3.6 0.4 - - - -
176A ALA* 3.2 15.7 + - + -
177A GLY 3.3 8.0 + - - -
178A GLN* 2.9 28.3 + - + +
179A ILE 4.0 1.3 - - - -
180A ALA* 4.0 20.4 - - + +
192A VAL* 4.0 26.9 - - + -
549A ARG 3.4 20.2 - - - +
550A LEU* 3.9 32.8 - - + -
551A VAL 3.2 22.2 - - - +
553A PRO* 4.6 1.8 - - + -
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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