Contacts of the helix formed by residues 110 - 124 (chain U) in PDB entry 5JPQ
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 ALA 110 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25U ALA* 3.7 33.0 - - + +
28U LYS* 4.1 9.2 - - + -
29U ALA* 4.9 0.2 - - + -
107U PRO* 3.5 20.0 - - + +
108U GLY 3.0 1.0 + - - -
109U GLU* 1.3 80.0 - - - +
111U LYS* 1.3 55.7 + - - +
112U ASP 3.3 2.2 - - - -
113U LEU* 3.0 12.0 + - + -
114U VAL* 2.7 36.8 + - + +
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Residues in contact with LYS 111 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107U PRO* 3.7 15.8 - - + +
108U GLY 3.4 13.5 + - - +
109U GLU 3.7 0.2 - - - -
110U ALA* 1.3 77.2 - - - +
112U ASP* 1.3 57.5 + - - +
114U VAL* 3.8 1.8 - - - +
115U ASP* 2.9 32.1 + - - +
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Residues in contact with ASP 112 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110U ALA 3.3 0.6 - - - -
111U LYS* 1.3 77.5 - - - +
113U LEU* 1.3 62.0 + - - +
115U ASP* 3.6 5.8 + - - +
116U GLU* 3.3 23.6 + - - +
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Residues in contact with LEU 113 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21U LYS* 5.5 5.4 - - - +
25U ALA* 4.6 16.2 - - + +
110U ALA* 3.0 21.3 + - + +
112U ASP* 1.3 80.1 - - - +
114U VAL* 1.3 60.0 + - - +
116U GLU* 3.6 6.2 + - - +
117U ILE* 3.4 18.9 + - - +
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Residues in contact with VAL 114 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25U ALA* 4.9 10.5 - - + +
52U LYS* 6.5 0.9 - - + -
53U LEU* 5.7 9.9 - - + -
107U PRO* 4.6 12.1 - - + -
110U ALA* 2.7 21.7 + - + +
111U LYS 3.8 3.8 - - - +
113U LEU* 1.3 70.7 - - - +
115U ASP* 1.3 58.7 + - - +
117U ILE* 2.9 10.0 + - - +
118U ILE* 2.9 30.3 + - - +
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Residues in contact with ASP 115 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111U LYS 2.9 18.7 + - - +
112U ASP* 4.1 6.3 - - - +
114U VAL* 1.3 75.1 - - - +
116U GLU* 1.3 60.7 + - - +
118U ILE* 3.8 6.3 + - - +
119U LYS* 3.4 23.4 + - - +
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Residues in contact with GLU 116 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112U ASP 3.3 17.5 + - - +
113U LEU* 3.8 6.5 - - - +
114U VAL 3.2 0.4 - - - -
115U ASP* 1.3 76.7 - - - +
117U ILE* 1.3 57.8 + - - +
119U LYS* 3.3 4.5 + - - +
120U ARG* 2.9 29.9 + - - +
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Residues in contact with ILE 117 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21U LYS* 5.9 5.6 - - + +
22U VAL* 5.8 10.3 - - + +
25U ALA* 6.1 2.7 - - + -
113U LEU 3.4 10.3 + - - +
114U VAL* 2.9 11.3 + - - +
116U GLU* 1.3 75.2 - - - +
118U ILE* 1.3 56.3 + - - +
119U LYS 3.0 9.4 + - - -
120U ARG* 3.2 6.4 + - - +
121U VAL* 3.0 27.4 + - - +
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Residues in contact with ILE 118 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52U LYS 5.5 4.7 - - - +
79U PRO* 4.6 22.9 - - + +
114U VAL 2.9 18.0 + - - +
115U ASP* 3.8 6.3 + - - +
117U ILE* 1.3 71.3 - - - +
119U LYS* 1.3 57.1 + - - +
121U VAL* 4.4 6.0 - - - +
122U ASN* 3.8 15.7 + - - +
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Residues in contact with LYS 119 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115U ASP 3.4 17.5 + - - +
116U GLU* 3.3 5.5 + - - +
117U ILE 3.0 0.8 - - - -
118U ILE* 1.3 78.4 - - - +
120U ARG* 1.3 62.3 + - - +
121U VAL 3.4 1.3 - - - -
122U ASN* 3.4 8.8 - - - +
123U GLU* 3.3 20.3 + - - +
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Residues in contact with ARG 120 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18U LEU* 5.9 7.0 - - + -
116U GLU 2.9 17.2 + - - +
117U ILE* 3.2 6.9 + - - +
119U LYS* 1.3 75.9 - - - +
121U VAL* 1.3 59.3 + - - +
122U ASN 3.2 0.4 - - - -
123U GLU* 3.3 8.1 + - - +
124U ILE* 3.1 27.9 + - - +
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Residues in contact with VAL 121 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79U PRO* 6.3 3.1 - - + -
80U TYR 4.7 14.4 - - - +
81U VAL* 5.7 6.3 - - + -
117U ILE 3.0 15.5 + - - +
118U ILE* 5.0 4.9 - - - +
120U ARG* 1.3 74.0 - - - +
122U ASN* 1.3 59.3 + - - +
124U ILE* 3.9 5.6 - - - +
125U LYS* 2.9 26.9 + - - +
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Residues in contact with ASN 122 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118U ILE 3.8 16.3 + - - +
119U LYS* 3.4 13.8 + - - +
121U VAL* 1.3 77.0 - - - +
123U GLU* 1.3 63.0 + - - +
125U LYS* 3.3 6.2 + - - +
126U GLY 3.2 22.5 + - - +
127U LYS* 3.4 19.9 - - + +
184W ARG* 5.4 0.2 - - - -
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Residues in contact with GLU 123 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119U LYS 3.3 11.2 + - - +
120U ARG* 3.3 10.3 + - - +
122U ASN* 1.3 74.5 - - - +
124U ILE* 1.3 48.1 - - + +
125U LYS 3.0 0.4 - - - -
126U GLY 4.0 4.3 - - - -
127U LYS* 5.2 0.4 - - - -
188W VAL* 0.9 111.8 - - - +
189W THR* 4.1 13.9 - - - +
190W LYS 4.8 3.6 - - - +
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Residues in contact with ILE 124 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12U PHE* 4.2 17.3 - - - +
13U GLU 4.8 13.1 + - - +
120U ARG 3.1 15.4 + - - +
121U VAL* 3.9 5.6 - - - +
122U ASN 3.4 0.2 - - - -
123U GLU* 1.3 69.0 - - + +
125U LYS* 1.3 53.9 + - - +
188W VAL* 1.6 20.4 - - - +
189W THR* 3.8 5.4 - - - +
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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