Contacts of the strand formed by residues 171 - 177 (chain D) in PDB entry 1CD9
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 LYS 171 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A GLY* 3.4 37.1 - - - +
134D SER* 3.5 4.1 + - - -
135D TRP* 3.0 66.7 + - + +
136D LYS* 5.8 0.2 - - - +
167D LEU* 6.2 0.2 - - - -
168D PRO* 3.7 10.3 - - + -
170D SER* 1.3 76.3 - - - +
172D ASP* 1.3 65.5 + - - +
173D GLN 4.0 18.5 + - - +
174D PHE* 4.3 15.3 - - + -
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Residues in contact with ASP 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D LEU* 3.0 25.3 - - - +
133D LEU 4.3 0.2 - - - -
134D SER* 3.4 9.4 + - - -
136D LYS* 5.1 8.5 + - - -
171D LYS* 1.3 75.4 - - - +
173D GLN* 1.3 64.8 + - + +
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Residues in contact with GLN 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU* 3.1 29.2 - - + +
132D TRP* 3.9 21.9 - - + +
133D LEU 3.3 5.6 - - - -
171D LYS* 4.0 13.4 + - - +
172D ASP* 1.3 82.4 - - + +
174D PHE* 1.3 61.7 + - - +
175D GLU* 4.7 7.9 + - - +
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Residues in contact with PHE 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLY 5.2 5.4 - - - -
7A ALA* 4.9 6.1 - - + -
70A LEU* 5.1 9.6 - - + -
132D TRP* 3.5 4.0 - - - -
133D LEU* 2.9 44.8 + - + +
135D TRP* 3.6 36.3 - + + -
150D LEU* 3.9 21.8 - - + -
164D VAL* 4.7 8.5 - - + -
167D LEU* 4.0 22.9 - - + -
171D LYS* 4.3 16.4 - - + -
173D GLN* 1.3 74.8 - - - +
175D GLU* 1.3 68.9 + - - +
176D LEU* 3.5 28.5 + - + -
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Residues in contact with GLU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D GLN* 5.2 2.7 - - - +
130D CYS* 3.9 21.4 - - - -
131D LEU 3.6 3.8 - - - +
132D TRP* 3.1 44.5 + - + +
173D GLN* 4.1 7.9 + - - +
174D PHE* 1.3 82.9 - - - +
176D LEU* 1.3 61.8 + - - +
177D CYS* 4.3 2.9 + - + +
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Residues in contact with LEU 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 5.5 8.1 - - + -
130D CYS* 3.6 2.0 - - - -
131D LEU* 2.9 39.5 + - + +
133D LEU* 4.6 3.4 - - + -
150D LEU* 4.6 7.0 - - + -
152D TYR* 3.6 49.4 - - + +
164D VAL* 4.8 5.2 - - + -
174D PHE* 3.5 25.2 + - + +
175D GLU* 1.3 75.0 - - - +
177D CYS* 1.3 70.1 + - - +
179D LEU* 3.7 24.4 - - + +
187D LEU* 4.3 20.0 - - + -
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Residues in contact with CYS 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D GLN* 5.3 0.2 - - - -
128D PRO 4.1 7.9 - - - -
129D GLY 3.4 11.9 - - - -
130D CYS* 2.0 54.1 - - - -
152D TYR* 4.6 6.2 + - - -
175D GLU* 4.2 3.3 + - + +
176D LEU* 1.3 82.3 - - - +
178D GLY* 1.3 63.0 + - - +
179D LEU* 3.4 7.1 - - - +
180D HIS* 6.3 0.2 - - - -
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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