Contacts of the strand formed by residues 48 - 54 (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 LEU 48 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B PRO* 1.3 79.0 - - - +
49B CYS* 1.3 63.9 + - - +
138B ILE 3.6 0.5 - - - +
139B ARG* 3.0 6.1 - - - -
140B THR* 2.9 46.1 + - + +
141B LYS 3.9 10.3 - - - +
142B LEU* 4.2 17.7 - - + +
145B LYS* 3.2 46.2 - - + +
148B VAL* 3.7 23.1 - - + +
167B ILE* 3.6 28.9 - - + -
168B SER 4.1 3.6 - - - +
169B LYS* 5.2 0.2 - - - +
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Residues in contact with CYS 49 (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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47B PRO 4.1 1.1 - - - -
48B LEU* 1.3 80.1 - - - +
50B GLY* 1.3 60.2 + - - +
51B HIS* 3.6 12.5 - - + +
138B ILE 3.3 5.6 - - - +
139B ARG* 3.7 27.4 - - - -
166B HIS 4.0 0.2 - - - +
167B ILE* 3.4 7.8 - - - +
168B SER 2.7 43.5 + - - +
169B LYS 4.0 11.4 - - - -
170B LYS 3.6 28.5 - - - +
171B TRP* 3.8 16.2 - - + -
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Residues in contact with GLY 50 (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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49B CYS* 1.3 74.3 - - - +
51B HIS* 1.3 63.8 + - - -
137B SER* 3.3 4.5 - - - -
138B ILE 2.8 32.8 + - - -
148B VAL* 3.7 13.7 - - - +
152B LEU* 3.5 9.2 - - - +
166B HIS 3.4 5.6 - - - -
167B ILE* 3.5 16.4 - - - -
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Residues in contact with HIS 51 (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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176A PHE* 3.3 31.9 - + + -
49B CYS* 3.6 15.4 - - + +
50B GLY* 1.3 71.9 + - - -
52B MET* 1.3 60.4 + - - +
53B VAL* 3.3 12.0 + - + -
90B ARG* 3.9 0.2 + - - -
134B VAL* 4.2 7.4 - - + +
136B MET 3.7 2.7 - - - -
137B SER* 2.8 31.3 + - - -
152B LEU* 3.7 5.6 - - - +
165B ILE* 3.4 4.0 - - - +
166B HIS* 2.6 56.5 + + + +
168B SER* 4.5 4.9 - - - -
170B LYS 2.8 24.5 + - - -
171B TRP* 3.2 28.3 - + - -
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Residues in contact with MET 52 (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* 1.3 70.7 - - - +
53B VAL* 1.3 59.5 + - - +
134B VAL* 4.6 0.9 - - - -
135B ILE* 2.9 33.9 + - + +
136B MET* 3.0 48.6 + - + +
152B LEU* 3.5 25.9 - - + +
155B ALA* 3.5 4.9 - - + -
156B LYS* 3.2 35.2 - - + +
159B PHE* 3.8 26.2 - - + -
163B GLN* 4.0 25.8 - - + -
164B LYS 3.5 5.4 - - - +
165B ILE* 4.8 1.3 - - + +
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Residues in contact with VAL 53 (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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176A PHE* 4.0 36.1 - - + +
51B HIS* 3.3 5.4 + - + +
52B MET* 1.3 72.8 - - - +
54B SER* 1.3 68.6 + - - +
132B GLY* 3.4 33.4 - - - +
133B GLN 3.7 3.6 - - - +
134B VAL* 4.3 4.5 - - + +
135B ILE* 4.8 0.7 - - - -
163B GLN* 3.6 1.1 - - - -
164B LYS* 2.7 53.1 + - + +
166B HIS* 4.1 20.6 - - + -
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Residues in contact with SER 54 (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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52B MET 3.7 2.6 + - - -
53B VAL* 1.3 76.3 - - - +
55B ASP* 1.3 57.0 + - - +
56B GLU* 2.6 32.1 + - - +
58B GLU* 5.5 0.7 - - - +
129B VAL* 3.1 30.2 - - - +
130B HIS 3.1 3.8 + - - -
132B GLY* 2.7 31.0 + - - -
133B GLN 2.7 15.0 + - - -
135B ILE* 3.7 16.0 - - - +
162B ARG 4.3 4.7 + - - -
163B GLN* 4.6 2.2 + - - -
164B LYS* 5.7 0.3 - - - +
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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