Contacts of the strand formed by residues 136 - 141 (chain A) in PDB entry 2JAJ
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 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU 3.8 0.3 - - - +
132A PHE* 3.4 5.4 - - - -
133A THR* 3.0 26.7 + - - +
134A GLY 3.9 0.6 - - - -
135A ARG* 1.3 78.3 - - - +
137A PHE* 1.3 67.1 + - - +
138A PHE* 3.7 24.3 - - + -
160A TYR* 4.5 6.1 - - - -
161A ALA* 3.3 27.7 - - + +
163A SER* 4.4 8.8 + - - -
203A MET 5.1 0.5 - - - +
204A SER* 2.6 34.9 + - - -
206A HIS* 2.9 12.3 + - + -
208A TYR* 2.6 30.8 + - - +
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Residues in contact with PHE 137 (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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81A VAL* 4.2 11.0 - - + -
82A VAL 5.8 0.2 - - - -
83A CYS* 3.8 17.7 - - + -
130A VAL* 3.5 26.7 - - + -
131A LEU 3.3 4.5 - - - +
132A PHE* 3.6 34.8 - + + -
136A GLU* 1.3 78.5 - - - +
138A PHE* 1.3 68.4 + - - +
139A VAL* 4.6 1.1 - - + -
153A LEU* 4.0 8.7 - - + -
157A PHE* 3.7 38.8 - + + -
160A TYR* 3.8 25.6 - + + -
161A ALA 2.7 11.9 + - - +
162A VAL* 3.4 26.9 - - + -
163A SER* 3.0 24.1 + - - -
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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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129A ASP 3.6 1.0 - - - +
130A VAL* 3.5 2.6 - - - +
131A LEU* 2.9 40.3 + - + +
133A THR* 3.9 26.5 - - + -
136A GLU* 3.6 35.2 - - - -
137A PHE* 1.3 74.4 - - - +
139A VAL* 1.3 61.9 + - - +
163A SER* 3.3 13.5 - - - +
165A VAL* 4.7 2.0 - - + -
173A LEU* 3.6 7.9 - - + +
185A ILE* 5.3 3.4 - - + -
200A MET* 3.4 63.7 - - + -
203A MET* 3.7 26.7 - - + -
204A SER* 3.9 6.3 - - - -
208A TYR* 4.2 9.9 - + - -
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Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 4.0 9.6 - - + -
129A ASP 3.3 5.8 - - - +
130A VAL* 4.4 13.9 - - + -
137A PHE* 4.6 3.6 - - + -
138A PHE* 1.3 78.7 - - - +
140A GLY* 1.3 74.0 + - - +
141A LEU* 3.5 1.1 + - + -
145A THR* 3.9 17.3 - - + -
150A ALA* 3.9 21.5 - - + -
153A LEU* 4.5 12.3 - - + -
162A VAL* 3.8 25.1 - - + -
163A SER 2.8 12.9 + - - +
164A THR* 3.1 9.0 - - + +
165A VAL* 3.0 21.2 + - - +
173A LEU* 4.1 1.3 - - - -
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Residues in contact with GLY 140 (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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129A ASP* 2.7 25.8 + - - +
139A VAL* 1.3 69.2 - - - +
141A LEU* 1.3 61.4 + - - -
142A SER 3.8 0.7 - - - -
145A THR* 3.3 29.3 - - - +
165A VAL 3.2 10.5 - - - -
167A VAL* 3.9 15.3 - - - -
173A LEU* 3.6 11.7 - - - +
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Residues in contact with LEU 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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139A VAL 4.6 0.2 - - - +
140A GLY* 1.3 73.0 - - - +
142A SER* 1.3 59.4 + - - +
145A THR* 3.5 4.5 - - + +
146A ASN* 3.5 9.4 - - - +
147A GLN* 3.5 48.7 - - + +
150A ALA* 4.1 4.5 - - + -
164A THR* 3.7 39.7 - - + +
165A VAL 2.9 12.3 + - - +
166A PRO* 3.6 11.8 - - + +
167A VAL 2.9 25.8 + - - +
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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