Contacts of the strand formed by residues 157 - 163 (chain A) in PDB entry 2PO5
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 HIS 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A PRO* 5.3 0.4 - - - -
69A THR* 3.3 32.3 - - + +
71A ILE* 4.0 9.2 - - + -
144A VAL* 3.2 24.2 - - + +
147A LEU* 3.4 42.6 - - + +
148A ASP* 2.9 33.5 + - - +
151A SER* 3.3 27.2 - - - -
154A THR* 2.6 27.8 + - - -
155A ALA* 3.5 5.6 - - + -
156A PRO* 1.3 77.0 - - - +
158A LYS* 1.3 62.8 + - - +
389A ILE* 4.5 5.5 - - + +
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Residues in contact with LYS 158 (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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67A PRO* 3.9 26.8 - - + +
69A THR 2.9 7.0 + - - +
70A GLY* 3.2 5.2 - - - -
71A ILE* 2.8 25.3 + - - +
144A VAL* 4.1 5.4 - - - -
157A HIS* 1.3 76.0 - - - +
159A TYR* 1.3 69.3 + - + +
160A TYR* 3.1 32.3 - - + +
176A GLU* 3.2 16.2 + - - -
180A ASP* 3.0 27.7 + - - -
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Residues in contact with TYR 159 (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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71A ILE* 3.3 9.9 - - - +
73A MET* 4.2 11.2 - - - -
137A SER* 3.5 23.3 + - - -
140A GLY* 3.6 16.2 - - - -
141A GLU* 3.1 43.9 + - + -
143A MET* 4.0 15.7 - - + -
144A VAL* 3.7 16.6 - - + +
158A LYS* 1.3 85.7 - - + +
160A TYR* 1.3 68.4 + - - +
161A ILE* 3.7 32.0 - - + +
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Residues in contact with TYR 160 (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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70A GLY* 3.8 12.8 - - - -
71A ILE 2.9 8.4 + - - +
72A LEU* 3.5 16.7 - - + -
73A MET* 2.8 29.6 + - - +
158A LYS* 3.1 42.6 - - + +
159A TYR* 1.3 79.8 - - - +
161A ILE* 1.3 64.3 + - - +
162A GLY 3.9 0.2 - - - -
173A ALA* 4.2 9.9 - - + -
176A GLU* 3.6 27.1 - - - -
177A MET* 3.5 39.9 - - + -
180A ASP* 2.7 38.9 + - - +
182A LEU* 3.6 11.0 - - + +
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Residues in contact with ILE 161 (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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73A MET* 3.9 4.3 - - + +
133A LYS* 4.2 16.4 - - + +
136A THR* 3.8 27.1 - - + -
137A SER* 3.4 26.0 - - - +
159A TYR* 3.7 23.6 - - + +
160A TYR* 1.3 74.7 - - - +
162A GLY* 1.3 59.7 + - - +
163A PHE* 3.6 35.7 - - + -
168A PRO* 3.1 37.4 - - + +
173A ALA* 3.5 13.0 - - - +
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Residues in contact with GLY 162 (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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72A LEU* 3.8 18.2 - - - +
73A MET 3.0 15.6 + - - +
74A LEU* 3.6 11.5 - - - +
75A ASN 3.4 19.2 + - - +
161A ILE* 1.3 73.8 - - - +
163A PHE* 1.3 62.5 + - - -
164A ARG 3.7 0.5 + - - -
168A PRO 3.8 2.7 - - - -
170A THR* 3.8 17.6 + - - -
173A ALA* 4.1 0.7 - - - -
202A SER* 5.1 0.5 + - - -
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Residues in contact with PHE 163 (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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73A MET 5.2 0.9 - - - -
75A ASN* 3.2 26.0 - - + -
77A GLY* 3.5 16.4 - - - -
78A GLY 5.0 2.9 - - - -
80A GLU* 5.9 1.1 - - + -
132A ILE* 3.8 25.8 - - + -
133A LYS* 3.8 33.2 - - + -
136A THR* 4.0 8.5 - - + -
161A ILE* 3.6 28.0 - - + -
162A GLY* 1.3 73.6 - - - +
164A ARG* 1.3 65.2 + - - +
166A VAL* 3.2 38.9 - - + +
167A HIS 3.8 13.7 - - - -
168A PRO* 2.8 10.2 + - + +
169A LEU* 3.2 6.9 - - - -
170A THR* 3.0 20.4 + - - -
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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