Contacts of the strand formed by residues 137 - 147 (chain A) in PDB entry 1PU5
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 GLY 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A MET* 4.0 10.1 - - - +
59A LYS* 4.3 6.1 - - - -
60A GLU 5.6 1.6 - - - -
135A THR 3.5 0.6 + - - -
136A THR* 1.3 78.3 - - - +
138A ASN* 1.3 64.9 + - - -
139A TYR* 3.4 8.4 - - - -
160A SER* 3.2 2.8 - - - -
161A LEU 2.8 33.8 + - - -
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Residues in contact with ASN 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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1A HIS 3.1 19.8 - - - +
2A MET* 3.6 10.3 - - - -
3A SER* 2.9 28.3 + - - +
59A LYS* 3.7 1.9 - - - +
60A GLU* 3.0 58.3 + - + +
65A TRP* 3.7 13.6 - - + -
137A GLY* 1.3 72.1 - - - -
139A TYR* 1.3 65.5 + - - +
159A ALA 3.9 3.1 - - - +
160A SER* 2.7 30.6 + - - +
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Residues in contact with TYR 139 (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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57A LEU* 4.5 14.1 - - + -
58A GLU 3.2 9.6 - - - +
59A LYS* 3.2 46.3 + - + +
65A TRP* 3.8 6.3 - - - -
68A ILE* 4.1 15.5 - - + -
130A LEU* 5.8 1.6 - - - +
134A LEU 3.5 3.8 + - - -
135A THR* 2.6 34.5 + - - -
137A GLY 3.4 19.5 - - - -
138A ASN* 1.3 76.6 - - - +
140A ARG* 1.3 63.1 + - - +
158A ALA* 3.5 4.0 - - - +
159A ALA* 2.8 36.3 + - + +
161A LEU* 3.6 27.8 - - + +
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Residues in contact with ARG 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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56A VAL 3.8 0.9 - - - +
57A LEU* 3.5 4.5 - - - +
58A GLU* 2.9 67.6 + - + +
65A TRP* 3.2 66.2 - - + +
139A TYR* 1.3 76.4 - - - +
141A ILE* 1.3 62.4 + - - +
157A ILE 3.1 12.6 - - - +
158A ALA* 4.5 6.3 - - + -
159A ALA 5.0 0.2 - - - +
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Residues in contact with ILE 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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55A LEU* 4.2 28.9 - - + -
56A VAL 3.2 14.8 - - - +
57A LEU* 4.2 20.4 - - + -
75A GLY 5.3 1.1 - - - +
140A ARG* 1.3 77.6 - - - +
142A GLU* 1.3 71.9 + - - +
143A SER* 4.8 3.6 - - - +
155A ILE* 3.8 1.3 - - + +
156A LYS* 3.3 5.0 - - - +
157A ILE* 2.9 63.6 + - + +
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Residues in contact with GLU 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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10A CYS* 4.9 0.5 - - - -
54A ASP 3.6 1.0 - - - +
55A LEU* 3.3 4.7 - - - -
56A VAL* 2.8 51.7 + - + +
141A ILE* 1.3 77.3 - - - +
143A SER* 1.3 64.1 + - - +
144A VAL* 3.6 20.6 - - + +
151A ARG* 5.1 1.9 + - - -
154A CYS* 4.1 18.7 - - - -
155A ILE 3.3 9.4 - - - +
156A LYS* 4.2 20.4 - - + +
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Residues in contact with SER 143 (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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53A VAL* 4.1 10.0 - - - +
54A ASP 3.4 3.4 - - - -
55A LEU* 3.1 27.5 - - - +
141A ILE* 4.2 4.9 - - - -
142A GLU* 1.3 75.1 - - - +
144A VAL* 1.3 64.3 + - - +
145A LEU* 6.0 0.5 - - - +
153A GLY 4.5 0.3 - - - -
154A CYS* 3.2 4.3 - - - +
155A ILE* 2.9 49.4 + - - +
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Residues in contact with VAL 144 (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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52A LYS 3.5 1.4 - - - +
53A VAL* 3.4 6.3 - - - +
54A ASP* 2.9 45.3 + - + +
142A GLU* 3.6 22.4 - - + +
143A SER* 1.3 78.3 + - - +
145A LEU* 1.3 71.2 + - - +
146A SER* 4.7 7.8 + - - +
151A ARG* 3.6 44.0 - - + +
153A GLY 3.5 8.1 - - - +
154A CYS* 3.9 5.4 - - - -
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Residues in contact with LEU 145 (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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17A ALA* 4.3 11.0 - - + -
47A LEU* 3.9 36.8 - - + -
51A LEU* 3.4 37.2 - - + -
52A LYS 3.4 8.7 - - - +
53A VAL* 3.8 16.6 - - + +
82A PHE* 5.8 0.2 - - + -
143A SER* 4.2 0.6 - - - +
144A VAL* 1.3 76.8 - - - +
146A SER* 1.3 61.5 + - - +
152A LEU* 2.8 30.8 + - + -
153A GLY* 2.8 20.2 + - - +
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Residues in contact with SER 146 (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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51A LEU* 3.6 5.2 - - - +
52A LYS* 2.8 55.9 + - - +
144A VAL* 4.7 9.4 + - - +
145A LEU* 1.3 76.3 - - - +
147A SER* 1.3 63.8 + - - +
149A GLY* 4.7 10.3 + - - -
150A LYS 3.2 19.3 - - - -
151A ARG* 4.3 3.1 - - - -
152A LEU* 3.8 6.1 - - - -
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Residues in contact with SER 147 (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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48A SER 3.9 11.4 + - - -
49A SER 4.5 0.5 + - - -
50A PRO* 2.8 30.3 + - - +
51A LEU* 4.7 0.7 - - - -
52A LYS* 4.8 0.7 - - - +
146A SER* 1.3 76.4 - - - +
148A SER* 1.3 68.0 + - - +
149A GLY 3.0 0.2 - - - -
150A LYS* 2.9 37.6 + - - +
152A LEU* 3.8 18.8 - - - +
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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