Contacts of the strand formed by residues 137 - 142 (chain A) in PDB entry 3P8P
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 GLU 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU 3.7 0.3 - - - +
133A PHE* 3.4 7.7 - - - -
134A THR* 3.1 26.8 + - - +
136A ARG* 1.3 87.3 + - - +
138A PHE* 1.3 65.8 + - - +
139A PHE* 3.3 34.4 - - + -
161A TYR* 4.0 8.6 - - - -
162A ALA* 3.2 26.6 - - + +
164A SER* 5.1 2.8 + - - -
204A MET 4.4 3.8 - - - +
205A SER* 3.0 31.6 + - - -
206A ASP 5.7 0.2 - - - -
209A TYR* 2.6 26.4 + - - +
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Residues in contact with PHE 138 (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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82A VAL* 4.3 12.1 - - + -
83A VAL 6.1 0.2 - - - -
84A CYS* 3.7 21.8 - - + -
131A VAL* 3.5 27.6 - - + -
132A LEU 3.5 1.6 - - - -
133A PHE* 3.5 37.9 - + + -
137A GLU* 1.3 77.4 - - - +
139A PHE* 1.3 71.2 + - - +
140A VAL* 4.1 1.1 - - + -
154A LEU* 4.2 8.1 - - + -
158A PHE* 3.6 40.2 - + + -
161A TYR* 4.0 15.0 - - + -
162A ALA 2.8 8.5 + - - +
163A VAL* 3.7 32.8 - - + -
164A SER* 3.2 20.9 + - - -
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Residues in contact with PHE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ASP 3.1 0.5 - - - +
131A VAL* 3.5 0.4 - - - -
132A LEU* 2.9 32.3 + - + +
134A THR* 3.5 34.3 - - + -
137A GLU* 3.3 35.0 - - + -
138A PHE* 1.3 78.2 - - - +
140A VAL* 1.3 62.7 + - - +
164A SER* 3.3 24.0 - - - +
166A VAL* 4.9 2.7 - - + -
174A LEU* 2.7 31.7 - - + +
186A ILE* 5.3 1.8 - - + -
201A MET* 3.7 59.0 - - + -
202A GLN* 5.1 0.4 - - + -
204A MET* 4.8 2.9 - - + -
205A SER* 4.7 2.0 - - - -
209A TYR* 4.2 9.4 - + - -
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Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 4.7 1.8 - - + -
130A ASP* 3.3 3.6 - - + +
131A VAL* 4.0 26.5 - - + -
138A PHE* 4.8 0.4 - - + -
139A PHE* 1.3 75.4 - - - +
141A GLY* 1.3 64.8 + - - +
142A LEU* 5.1 0.2 - - + -
146A THR* 3.6 29.8 - - + -
151A ALA* 3.9 24.9 - - + +
154A LEU* 4.3 14.8 - - + -
163A VAL* 3.8 24.0 - - + -
164A SER 3.0 5.5 + - - -
165A THR* 3.0 10.0 - - + -
166A VAL 2.9 21.2 + - - -
174A LEU* 4.0 0.9 - - - -
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Residues in contact with GLY 141 (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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130A ASP* 2.8 24.9 + - - +
140A VAL* 1.3 73.8 - - - +
142A LEU* 1.3 63.6 + - - -
143A SER 3.4 1.3 + - - -
146A THR* 3.3 23.7 - - - +
166A VAL* 3.1 12.6 - - - -
168A VAL* 3.7 16.6 - - - -
174A LEU* 3.5 8.4 - - - +
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Residues in contact with LEU 142 (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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140A VAL* 3.5 0.6 + - + -
141A GLY* 1.3 73.0 - - - +
143A SER* 1.3 57.7 + - - +
146A THR* 3.4 8.5 - - + +
147A ASN* 3.4 36.6 - - - +
148A GLN* 3.7 24.7 - - - +
151A ALA* 4.6 1.6 - - + -
165A THR* 3.6 40.6 - - + +
166A VAL 3.0 10.3 + - - +
167A PRO* 3.9 10.1 - - + +
168A VAL 3.0 23.7 + - - +
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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