Contacts of the strand formed by residues 132 - 137 (chain D) in PDB entry 3P3W
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 132 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131D GLU* 1.3 79.3 + - + +
133D PHE* 1.3 63.4 + - - +
159D GLN* 3.8 26.0 - - + +
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Residues in contact with PHE 133 (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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125D LEU* 4.2 29.2 - - + -
130D TRP* 3.7 44.0 - + + -
131D GLU 4.0 9.4 - - - -
132D LYS* 1.3 77.4 - - - +
134D VAL* 1.3 79.2 + - - +
135D TYR* 4.6 18.6 - + + -
149D ILE* 5.0 8.3 - - + -
158D TRP* 4.3 13.0 - - + -
159D GLN 3.1 18.6 + - - +
160D VAL* 3.8 29.8 - - + -
161D THR* 3.6 13.7 + - - -
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Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D TRP* 5.7 0.9 - - - -
133D PHE* 1.3 89.7 - - - +
135D TYR* 1.3 67.7 + - - +
136D LEU* 4.3 21.2 + - + +
161D THR* 3.8 14.1 - - - +
163D ARG* 6.0 1.3 - - + -
177D ILE* 6.4 0.7 - - + -
181D MET* 3.9 39.0 - - + -
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Residues in contact with TYR 135 (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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121D ILE* 6.5 0.7 - - + -
133D PHE* 4.1 10.2 + + + -
134D VAL* 1.3 75.0 - - - +
136D LEU* 1.3 70.0 + - - +
137D TYR* 3.3 32.7 - + + +
145D VAL* 3.4 31.0 - - + +
146D LEU* 3.5 32.6 - - + +
149D ILE* 4.1 24.5 - - + -
160D VAL* 3.7 24.9 - - + -
161D THR 2.9 21.6 + - - +
162D ALA* 3.6 19.7 - - + -
163D ARG 2.9 14.2 + - - -
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Residues in contact with LEU 136 (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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134D VAL* 4.3 17.9 + - + -
135D TYR* 1.3 88.9 - - - +
137D TYR* 1.3 60.5 + - - +
138D ASP 4.3 0.2 + - - -
163D ARG* 3.7 26.0 - - + -
165D VAL* 3.8 30.3 - - + +
174D PHE* 6.0 4.0 - - + -
177D ILE* 4.8 12.6 - - + -
178D ILE* 6.0 6.3 - - + -
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Residues in contact with TYR 137 (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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146B LEU* 4.2 3.8 + - + +
147B GLN* 3.4 42.9 - - + +
150B MET* 3.1 22.9 - - - +
135D TYR* 3.3 39.0 - + + +
136D LEU* 1.3 74.3 - - - +
138D ASP* 1.3 69.1 + - - +
139D THR* 5.7 0.9 - - + -
145D VAL* 6.2 0.4 - - + -
146D LEU* 3.8 24.9 - - + -
162D ALA* 3.6 19.5 - - + -
163D ARG 3.1 21.7 + - - +
164D SER* 3.7 12.5 + - - -
165D VAL* 3.0 27.1 + - - -
166D GLY 3.8 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