Contacts of the helix formed by residues 114 - 123 (chain B) in PDB entry 2PH4
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 ASP 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B TYR* 2.9 32.1 + - - +
39B ASP* 4.6 0.2 - - - +
112B THR 3.8 5.6 - - - +
113B TYR* 1.3 75.6 - - - +
115B LYS* 1.3 57.5 + - - +
116B ASN* 3.0 38.4 + - - +
117B TYR* 2.9 38.1 + - + -
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Residues in contact with LYS 115 (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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69A LYS* 4.9 4.9 - - - +
70A LYS* 6.1 2.8 - - - +
21B TYR* 3.9 13.1 + - - -
113B TYR* 3.7 13.7 + - + -
114B ASP* 1.3 71.5 + - - +
116B ASN* 1.3 64.4 + - - +
118B ARG* 3.0 48.4 + - - +
119B PHE* 3.3 10.6 - - + -
304B SO4 2.6 44.1 + - - +
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Residues in contact with ASN 116 (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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114B ASP* 3.0 24.1 + - - +
115B LYS* 1.3 79.1 - - - +
117B TYR* 1.3 57.2 + - + +
118B ARG 3.1 0.7 - - - -
119B PHE* 2.9 36.1 + - - +
122B LYS* 4.2 24.2 + - + +
123B PHE* 4.1 3.3 - - - -
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Residues in contact with TYR 117 (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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25B TYR* 3.3 36.0 - + + -
26B GLY* 2.6 30.4 + - - +
38B LYS* 3.5 51.8 + - + +
39B ASP* 3.7 16.8 - - + -
114B ASP* 2.9 32.9 + - + +
116B ASN* 1.3 74.7 - - + +
118B ARG* 1.3 59.6 + - - +
119B PHE 3.2 1.3 - - - -
120B THR* 5.0 0.5 + - - -
123B PHE* 3.3 36.6 - + + -
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Residues in contact with ARG 118 (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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31A VAL* 3.6 32.2 - - + +
32A GLY* 3.7 16.5 - - - +
301A SO4 4.6 3.2 + - - -
20B THR* 3.6 10.6 + - - +
21B TYR* 3.0 44.3 - - - -
24B LEU* 3.6 28.4 - - - +
25B TYR* 4.5 0.2 - - + -
113B TYR* 2.9 31.4 + - - +
114B ASP 4.1 0.4 + - - -
115B LYS* 3.0 33.8 + - - +
117B TYR* 1.3 76.2 - - - +
119B PHE* 1.3 66.3 + - + +
120B THR* 3.0 17.6 + - - -
304B SO4 2.9 32.7 + - - -
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Residues in contact with PHE 119 (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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32A GLY* 3.3 37.0 - - - -
34A ARG* 3.4 35.0 - - + -
301A SO4 3.6 18.6 - - - -
302A SO4 4.9 0.9 - - - -
115B LYS* 3.3 26.0 - - + -
116B ASN* 2.9 18.1 + - - +
118B ARG* 1.3 79.1 - - + +
120B THR* 1.3 52.5 + - - +
121B MET* 2.8 9.0 + - + +
122B LYS* 2.5 71.9 + - + +
123B PHE* 3.2 10.8 - - - -
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Residues in contact with THR 120 (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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32A GLY 4.4 0.6 + - - -
33A ARG* 3.9 23.6 - - - +
120A THR* 4.9 4.5 - - + +
121A MET* 5.4 2.9 - - + -
24B LEU* 3.6 23.8 - - + +
26B GLY 4.5 0.9 + - - -
33B ARG* 3.4 35.3 + - - +
117B TYR 5.0 0.7 + - - -
118B ARG 3.0 7.9 + - - -
119B PHE* 1.3 72.7 - - - +
121B MET* 1.3 65.3 + - + +
123B PHE* 3.1 35.9 - - - +
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Residues in contact with MET 121 (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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32A GLY 3.0 28.5 - - - +
33A ARG* 3.6 22.0 - - - +
34A ARG* 2.8 47.3 - - + +
126A CYS* 4.3 15.7 - - + +
119B PHE* 2.8 3.7 + - + -
120B THR* 1.3 84.6 - - + +
122B LYS* 1.3 58.7 + - + +
123B PHE 3.3 7.7 + - - +
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Residues in contact with LYS 122 (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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34A ARG* 6.2 0.9 - - - -
302A SO4 4.8 10.4 + - - -
116B ASN* 4.2 24.8 + - + +
119B PHE* 2.5 59.6 + - + +
121B MET* 1.3 74.1 - - + +
123B PHE* 1.3 60.3 + - - +
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Residues in contact with PHE 123 (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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26B GLY* 3.2 39.3 - - - -
27B CYS* 3.9 0.9 - - - -
33B ARG* 3.6 14.4 - - - -
38B LYS* 3.6 23.8 - - - +
116B ASN 4.1 4.7 - - - -
117B TYR* 3.3 48.2 - + + -
119B PHE 3.2 32.3 - - - -
120B THR* 3.1 24.0 - - - +
121B MET* 3.3 4.0 + - - -
122B LYS* 1.3 80.9 - - - +
125B LEU* 1.3 72.4 + - - +
126B CYS* 3.8 6.8 - - - -
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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