Contacts of the strand formed by residues 164 - 170 (chain A) in PDB entry 2P9R
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 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A ARG* 3.5 40.2 - - + +
125A VAL 3.0 15.0 - - - +
126A VAL* 3.7 12.6 - - + -
160A LEU* 3.7 8.5 - - - +
161A GLU* 2.9 30.5 + - - +
162A GLY* 2.9 24.5 - - - +
163A GLY* 1.3 81.3 - - - +
165A LYS* 1.3 63.5 + - - +
166A GLN* 6.4 0.2 - - + -
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Residues in contact with LYS 165 (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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124A ARG* 3.4 4.2 - - - -
125A VAL* 2.9 45.8 + - + +
158A PHE* 3.5 33.2 - - + -
159A GLN 4.3 10.7 + - - +
160A LEU* 3.9 8.3 - - + -
161A GLU* 5.2 6.8 + - + +
164A LEU* 1.3 80.2 - - - +
166A GLN* 1.3 68.2 + - - +
167A PHE* 3.7 22.4 - - + -
169B PHE* 5.8 5.4 - - - -
170B PRO* 4.2 24.7 + - - +
171B LEU 4.9 5.9 + - - -
172B SER* 5.0 11.5 - - - +
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Residues in contact with GLN 166 (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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122A LYS* 5.1 16.4 + - + +
123A PHE 3.5 13.2 - - - +
124A ARG* 3.2 31.6 - - + +
164A LEU* 6.4 0.2 - - + -
165A LYS* 1.3 80.7 + - - +
167A PHE* 1.3 79.6 + - - +
170B PRO* 4.8 12.3 - - - +
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Residues in contact with PHE 167 (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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122A LYS* 3.4 4.0 - - - +
123A PHE* 2.8 67.4 + + + +
125A VAL* 3.6 28.5 - - + -
142A VAL* 4.0 1.3 - - + -
155A TRP* 3.4 52.7 - + + -
158A PHE* 3.5 35.7 - + + -
165A LYS* 3.7 26.9 - - + -
166A GLN* 1.3 83.6 - - - +
168A SER* 1.3 62.2 + - - +
169B PHE* 5.7 1.6 - + - -
170B PRO* 6.0 5.2 - - + -
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Residues in contact with SER 168 (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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120A THR* 3.8 12.9 + - - -
121A VAL 3.1 10.8 - - - -
122A LYS* 4.0 15.3 - - - -
123A PHE* 5.4 1.3 - - - -
155A TRP* 3.9 15.5 - - - -
167A PHE* 1.3 78.9 - - - +
169A PHE* 1.3 62.7 + - - +
170A PRO* 4.2 7.9 - - - +
155B TRP* 5.5 1.0 + - - -
168B SER* 4.9 10.0 + - - +
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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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120A THR* 4.0 1.3 + - - -
121A VAL* 2.7 39.0 + - + +
144A ILE* 3.6 28.0 - - + -
152A ILE* 3.4 56.3 - - + -
153A ALA* 3.7 13.7 - - + -
155A TRP* 4.6 3.1 - + + -
168A SER* 1.3 75.0 - - - +
170A PRO* 1.3 84.0 - - + +
171A LEU* 3.3 19.9 + - + -
172A SER 6.1 0.2 - - - -
196A PHE* 6.2 0.2 - + - -
155B TRP* 3.8 19.1 - + - -
158B PHE* 6.3 3.1 - - + -
165B LYS* 5.7 5.8 - - - -
167B PHE* 5.5 3.8 - + - -
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Residues in contact with PRO 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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119A GLN 4.1 0.2 - - - +
120A THR* 3.9 19.5 - - - +
168A SER* 4.2 7.9 - - - +
169A PHE* 1.3 103.6 - - + +
171A LEU* 1.3 67.9 + - - +
172A SER 3.7 1.0 + - - -
155B TRP* 5.8 2.2 - - - +
165B LYS* 4.3 16.9 + - - +
166B GLN 5.2 10.5 - - - +
167B PHE* 6.1 7.0 - - + -
168B SER* 6.1 1.1 - - - +
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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