Contacts of the strand formed by residues 112 - 118 (chain X) in PDB entry 2PMO
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 112 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14X LEU* 4.0 5.3 - - + +
16X LYS* 3.0 30.5 + - - -
56X LYS* 4.0 10.6 + - - -
57X TYR 3.5 8.7 - - - +
58X GLU* 4.3 16.2 - - + +
107X ILE 3.9 0.2 - - - +
108X THR* 2.6 30.2 + - - -
109X ASN* 2.7 25.7 + - - +
111X ASP* 1.3 83.2 - - + +
113X VAL* 1.3 55.5 + - - +
114X TYR* 2.5 42.1 + - + -
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Residues in contact with VAL 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X MET* 3.6 27.1 - - + -
55X LYS 3.4 0.6 - - - +
56X LYS* 3.3 5.4 - - - +
57X TYR* 2.9 38.4 + - + +
85X PHE* 3.7 28.3 - - + -
89X LEU* 5.0 3.8 - - + -
106X ILE* 3.9 24.7 - - + -
107X ILE 3.4 2.2 - - - -
108X THR* 3.3 16.6 - - - +
111X ASP 4.2 2.0 - - - +
112X GLU* 1.3 72.4 - - - +
114X TYR* 1.3 68.1 + - - +
115X ILE* 3.9 18.6 - - + -
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Residues in contact with TYR 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X LEU* 3.9 22.4 - - + -
16X LYS* 3.6 11.4 - - - +
25X ILE* 3.6 35.1 - - + +
43X ILE* 4.3 6.3 - - + -
54X LEU* 4.2 19.5 - - + -
55X LYS 3.3 4.5 - - - +
56X LYS* 3.3 43.7 + - + -
105X GLY 4.0 0.2 - - - +
106X ILE* 3.4 4.7 - - - +
107X ILE* 2.6 57.7 + - + +
112X GLU* 2.5 41.9 + - + -
113X VAL* 1.3 79.0 - - - +
115X ILE* 1.3 63.0 + - - +
116X ILE 4.0 0.5 + - - -
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Residues in contact with ILE 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53X ALA 3.4 1.6 - - - +
54X LEU* 3.2 6.6 - - - -
55X LYS* 3.0 30.9 + - + +
57X TYR* 3.7 21.5 - - + -
89X LEU* 4.1 13.0 - - + -
92X ILE* 3.6 35.7 - - + -
103X CYS* 3.4 31.0 - - + -
105X GLY 3.9 2.5 - - - +
106X ILE* 3.9 14.6 - - + +
113X VAL* 3.9 7.2 - - + -
114X TYR* 1.3 76.5 - - - +
116X ILE* 1.3 61.0 + - - +
117X TYR* 3.4 27.3 + - + +
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Residues in contact with ILE 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X ILE* 4.0 10.3 - - + -
28X TYR* 3.5 36.1 - - + +
52X TYR* 4.1 20.6 - - + -
53X ALA 4.0 1.3 - - - -
54X LEU* 4.3 16.8 - - + -
103X CYS* 3.3 4.2 - - - -
104X GLU* 2.7 42.0 + - + +
105X GLY* 2.9 32.1 + - - +
107X ILE* 3.8 34.5 - - + -
114X TYR 4.7 0.7 - - - +
115X ILE* 1.3 72.7 - - - +
117X TYR* 1.3 61.1 + - - +
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Residues in contact with TYR 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52X TYR* 3.7 10.1 - - - +
53X ALA 2.8 36.0 + - - +
55X LYS* 4.1 15.3 - - + +
92X ILE* 3.9 25.3 - - + +
101X LEU* 3.6 30.0 + - + -
102X THR 3.6 16.8 - - - -
103X CYS* 3.5 24.9 - - + -
104X GLU* 4.3 4.5 - - - -
115X ILE* 3.4 30.3 + - + +
116X ILE* 1.3 74.5 - - - +
118X GLU* 1.3 61.1 + - - +
190X ASP* 5.8 1.8 + - - -
191X PHE* 5.0 6.8 - + - -
400X HMD 3.2 48.0 - - + -
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Residues in contact with GLU 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X LYS* 6.5 0.7 - - - -
51X PHE 5.1 0.7 - - - -
52X TYR* 5.1 4.0 - - - +
53X ALA 4.4 0.2 - - - -
100X CYS 5.2 0.2 - - - +
101X LEU* 4.0 12.1 - - + +
102X THR 5.0 7.5 + - - +
104X GLU* 3.7 21.4 + - - +
117X TYR* 1.3 74.6 - - - +
119X TYR* 1.3 62.3 + - - +
120X MET* 3.6 26.4 + - - +
181X ASP* 5.0 5.7 - - - +
185X ARG* 5.7 0.5 + - - -
187X LYS* 3.2 32.0 - - - +
400X HMD 3.0 23.4 + - - -
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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