Contacts of the strand formed by residues 134 - 140 (chain B) in PDB entry 2PA2
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 VAL 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A THR* 3.1 30.7 + - + +
175A LYS* 4.4 1.1 - - - +
176A PHE* 3.3 38.6 - - + -
51B HIS* 4.2 9.0 - - + -
52B MET 3.8 5.2 - - - +
53B VAL* 4.3 5.2 - - + +
90B ARG* 4.0 17.7 - - + +
91B LEU* 3.4 16.5 - - - +
133B GLN* 1.3 74.9 + - - +
135B ILE* 1.3 64.2 + - - +
136B MET 3.8 12.3 - - - +
137B SER* 3.3 25.8 - - - +
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B MET* 2.9 22.1 + - - +
54B SER* 3.7 33.2 - - - +
60B LEU* 4.4 14.6 - - + -
65B LEU* 4.1 12.1 - - + -
89B VAL* 3.8 2.7 - - + +
90B ARG* 2.9 23.3 + - - -
91B LEU* 3.8 16.2 - - + +
129B VAL* 4.1 8.5 - - + -
133B GLN 3.9 0.2 - - - +
134B VAL* 1.3 74.6 - - - +
136B MET* 1.3 66.0 + - + +
159B PHE* 3.7 30.1 - - + -
163B GLN* 3.8 28.3 - - + +
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Residues in contact with MET 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B HIS* 3.7 0.3 - - - -
52B MET* 3.0 52.4 + - + +
65B LEU 5.1 1.1 - - - +
68B ALA* 3.4 45.5 - - + +
69B ARG* 4.3 10.5 - - - +
72B ALA* 4.6 1.8 - - - -
87B ILE* 4.5 15.9 - - + -
88B ARG 3.4 14.4 - - - +
89B VAL* 3.8 13.9 - - + -
90B ARG* 4.1 2.0 - - - +
134B VAL* 3.7 3.0 - - - +
135B ILE* 1.3 83.4 - - + +
137B SER* 1.3 66.7 + - - +
152B LEU* 4.2 19.0 - - + +
155B ALA* 3.9 1.3 - - + -
159B PHE* 3.8 10.3 - - + -
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLY 3.3 4.3 - - - -
51B HIS* 2.8 22.4 + - - -
87B ILE* 3.5 4.4 - - - +
88B ARG 3.0 32.4 + - - -
90B ARG* 2.8 30.0 + - - +
134B VAL* 3.3 2.9 - - - +
136B MET* 1.3 77.2 - - - +
138B ILE* 1.3 64.7 + - - +
152B LEU* 5.5 0.4 - - - -
171B TRP* 3.4 28.4 - - - -
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Residues in contact with ILE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU 3.6 0.5 - - - +
49B CYS* 3.3 3.3 - - - -
50B GLY 2.8 32.0 + - - +
72B ALA* 4.7 0.9 - - + -
76B MET* 3.9 34.5 - - + -
85B PHE* 4.3 6.3 - - + -
86B HIS 3.3 9.4 - - - +
87B ILE* 3.8 21.8 - - + -
137B SER* 1.3 79.4 - - - +
139B ARG* 1.3 70.0 + - - +
148B VAL* 4.0 17.7 - - + +
151B ALA* 3.9 23.3 - - + -
152B LEU* 3.7 31.2 - - + -
171B TRP* 3.8 3.2 - - - -
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Residues in contact with ARG 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ALA* 5.8 3.2 - - - +
42B LYS* 3.5 20.2 + - - +
43B VAL* 3.7 35.7 + - - +
46B PHE* 2.7 43.6 + - + +
47B PRO* 4.3 2.8 + - - +
48B LEU 3.0 7.6 - - - +
49B CYS* 3.7 12.2 - - - -
85B PHE* 3.4 2.1 - - - +
86B HIS* 2.9 63.7 + - + -
138B ILE* 1.3 76.1 - - - +
140B THR* 1.3 64.5 + - - +
169B LYS 5.4 1.8 + - - -
171B TRP* 3.6 48.3 - - + +
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Residues in contact with THR 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 3.2 22.7 - - - +
48B LEU* 2.9 36.9 + - + +
76B MET* 4.5 4.1 - - + +
84B GLY 2.7 22.4 + - - -
85B PHE* 4.1 7.8 - - - +
139B ARG* 1.3 75.8 - - - +
141B LYS* 1.3 75.9 + - - +
144B ASN* 3.1 21.4 + - + +
148B VAL* 3.4 32.5 - - + -
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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