Contacts of the strand formed by residues 169 - 172 (chain A) in PDB entry 3HPD
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 ASP 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A VAL 3.6 6.5 - - - +
165A THR* 3.1 13.4 - - - +
166A GLY 2.9 31.6 + - - +
167A ALA 5.1 0.2 - - - +
168A VAL* 1.3 75.8 - - - +
170A TYR* 1.3 62.9 + - - +
171A VAL* 5.0 0.4 - - - -
178A PHE 3.7 0.2 - - - +
179A ALA* 3.3 5.2 - - - -
180A VAL* 2.8 57.0 + - + +
182A ASN 4.2 8.8 - - - +
218A LEU* 3.8 34.1 - - + +
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Residues in contact with TYR 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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144A GLU* 2.9 52.8 - - + +
147A ALA* 3.8 20.0 - - + -
148A LYS* 4.0 21.3 - - + -
151A THR* 3.4 24.5 - - + +
163A ALA* 3.1 4.2 - - - +
164A VAL 2.9 35.1 + - - +
168A VAL* 3.8 25.7 - - + +
169A ASP* 1.3 75.4 - - - +
171A VAL* 1.3 63.5 + - - +
177A THR* 4.3 9.9 - - + -
178A PHE 3.3 11.7 - - - -
179A ALA* 3.6 19.6 - - + +
181A TYR* 5.0 3.6 + - - -
261A ARG* 5.9 0.6 + - - -
263A VAL* 4.4 9.4 - - + -
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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
----------------------------------------------------------
151A THR* 3.9 0.2 - - - -
161A THR* 3.9 6.3 - - + -
162A VAL 3.3 10.1 - - - +
163A ALA* 4.2 1.8 - - + -
170A TYR* 1.3 80.5 - - - +
172A SER* 1.3 63.9 + - - +
177A THR* 3.2 4.2 - - - +
178A PHE* 2.8 36.0 + - + +
180A VAL* 4.8 5.4 - - + -
211A LEU* 3.6 19.2 - - + +
214A THR* 3.8 26.9 - - + -
215A THR* 3.8 21.5 - - - +
218A LEU* 3.4 31.6 - - + -
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Residues in contact with SER 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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151A THR* 3.5 16.4 - - - +
152A MET* 4.1 15.3 - - - +
155A ALA* 3.4 4.9 - - - +
161A THR* 3.3 1.7 - - - -
162A VAL 2.8 33.5 + - - +
171A VAL* 1.3 75.5 - - - +
173A ASP* 1.3 59.4 + - - +
174A GLY* 3.0 17.7 + - - -
176A ARG 3.0 10.4 + - - -
177A THR* 2.9 26.3 + - - -
211A LEU* 3.9 5.8 - - - -
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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