Contacts of the helix formed by residues 110 - 124 (chain V) 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 V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25V ALA* 3.9 9.2 - - + +
29V ALA* 4.9 0.4 - - + -
107V PRO* 3.4 19.3 - - + +
108V GLY 3.0 0.6 + - - -
109V GLU* 1.3 74.3 - - - +
111V LYS* 1.3 58.0 + - - +
112V ASP 3.2 2.7 - - - -
113V LEU 2.9 2.5 + - - -
114V VAL* 2.7 36.3 + - + +
184u SER* 2.9 34.5 - - - -
185u GLY* 3.0 15.0 - - - +
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Residues in contact with LYS 111 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107V PRO* 3.8 14.9 - - + +
108V GLY 3.4 14.1 + - - +
109V GLU 3.7 0.2 - - - -
110V ALA* 1.3 77.5 - - - +
112V ASP* 1.3 58.3 + - - +
114V VAL* 3.4 2.0 + - - +
115V ASP* 2.9 32.0 + - - +
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Residues in contact with ASP 112 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110V ALA 3.2 0.6 - - - -
111V LYS* 1.3 78.3 - - - +
113V LEU* 1.3 61.1 + - - +
115V ASP* 3.5 6.3 + - - +
116V GLU* 3.3 22.7 + - - +
185u GLY 5.1 6.3 - - - -
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Residues in contact with LEU 113 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21V LYS* 5.4 5.2 - - - +
25V ALA* 4.7 4.5 - - + +
110V ALA 2.9 1.4 + - - +
112V ASP* 1.3 78.1 - - - +
114V VAL* 1.3 63.2 + - - +
116V GLU* 3.6 6.7 + - - +
117V ILE* 3.4 18.2 + - - +
184u SER 3.4 4.0 - - - +
185u GLY* 1.4 61.2 - - - +
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Residues in contact with VAL 114 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25V ALA* 4.9 10.8 - - + +
52V LYS* 6.5 1.1 - - + -
53V LEU* 5.6 10.1 - - + -
107V PRO* 4.6 12.8 - - + -
110V ALA* 2.7 21.6 + - + +
111V LYS* 3.8 3.6 - - - +
113V LEU* 1.3 71.0 - - - +
115V ASP* 1.3 59.8 + - - +
116V GLU 3.1 0.4 - - - -
117V ILE* 2.9 9.9 + - - +
118V ILE* 2.8 30.4 + - - +
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Residues in contact with ASP 115 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111V LYS 2.9 19.4 + - - +
112V ASP* 3.9 7.0 - - - +
113V LEU 3.4 0.2 - - - -
114V VAL* 1.3 76.0 - - - +
116V GLU* 1.3 60.3 + - - +
118V ILE* 4.6 4.5 - - - +
119V LYS* 3.4 3.3 + - - +
188X VAL* 3.2 41.8 - - + +
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Residues in contact with GLU 116 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112V ASP 3.3 12.6 + - - +
113V LEU* 3.7 10.1 - - - +
114V VAL 3.1 0.4 - - - -
115V ASP* 1.3 76.7 - - - +
117V ILE* 1.3 58.4 + - - +
119V LYS* 3.4 4.4 + - - +
120V ARG* 2.9 29.9 + - - +
87u SER* 6.1 5.8 - - - -
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Residues in contact with ILE 117 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18V LEU 6.2 0.2 - - - +
21V LYS* 5.9 5.8 - - + +
22V VAL* 5.8 10.5 - - + +
25V ALA* 6.1 2.9 - - + -
113V LEU 3.4 9.6 + - - +
114V VAL* 2.9 11.9 + - - +
116V GLU* 1.3 74.4 - - - +
118V ILE* 1.3 58.7 + - - +
119V LYS 2.9 9.8 + - - -
120V ARG* 3.1 5.4 + - - +
121V VAL* 3.0 25.9 + - - +
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Residues in contact with ILE 118 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52V LYS 5.7 3.1 - - - +
79V PRO* 4.6 21.6 - - + +
114V VAL 2.8 17.8 + - - +
115V ASP* 3.8 5.8 + - - +
117V ILE* 1.3 72.3 - - - +
119V LYS* 1.3 55.7 + - - +
121V VAL* 4.3 6.4 - - - +
122V ASN* 3.8 15.8 + - - +
184X ARG* 4.1 13.4 - - + +
188X VAL* 3.7 8.0 - - + +
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Residues in contact with LYS 119 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115V ASP 3.4 8.0 + - - +
116V GLU* 3.4 5.1 + - - +
117V ILE 2.9 0.8 - - - -
118V ILE* 1.3 79.1 - - - +
120V ARG* 1.3 62.1 + - - +
121V VAL 3.4 0.7 - - - -
122V ASN* 3.5 8.2 - - - +
123V GLU* 3.4 18.9 + - - +
188X VAL* 2.2 46.2 + - + +
189X THR* 3.8 5.6 - - - +
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Residues in contact with ARG 120 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18V LEU* 5.8 7.9 - - + -
116V GLU 2.9 17.4 + - - +
117V ILE* 3.9 5.8 - - - +
119V LYS* 1.3 76.8 - - - +
121V VAL* 1.3 56.5 + - - +
122V ASN 3.2 0.4 - - - -
123V GLU* 3.3 7.5 + - - +
124V ILE* 3.1 28.4 + - - +
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Residues in contact with VAL 121 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79V PRO* 6.2 3.6 - - + -
80V TYR 4.8 13.9 - - - +
81V VAL* 5.6 7.0 - - + -
117V ILE 3.0 14.8 + - - +
118V ILE* 5.0 4.5 - - - +
120V ARG* 1.3 72.9 - - - +
122V ASN* 1.3 60.2 + - - +
124V ILE* 4.0 6.2 - - - +
125V LYS* 2.9 25.8 + - - +
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Residues in contact with ASN 122 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118V ILE 3.8 16.6 + - - +
119V LYS* 3.5 13.6 + - - +
121V VAL* 1.3 78.1 - - - +
123V GLU* 1.3 63.8 + - - +
125V LYS* 3.2 6.6 + - - +
126V GLY 3.1 25.6 + - - +
127V LYS* 3.5 17.2 - - + +
184X ARG 4.7 9.0 - - - +
185X SER* 5.2 7.0 - - - +
186X ILE 5.9 1.1 - - - +
187X ASP* 6.0 1.8 - - - -
188X VAL 5.6 2.5 - - - +
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Residues in contact with GLU 123 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119V LYS 3.4 9.9 + - - +
120V ARG* 3.3 11.2 + - - +
122V ASN* 1.3 75.9 - - - +
124V ILE* 1.3 57.2 + - + +
125V LYS 3.0 9.4 + - - -
126V GLY* 3.3 19.1 + - - +
127V LYS* 5.3 0.4 - - - -
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Residues in contact with ILE 124 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12V PHE* 4.3 16.0 - - + +
13V GLU 4.8 13.1 + - - +
120V ARG 3.1 14.9 + - - +
121V VAL* 4.0 4.9 - - - +
122V ASN 3.4 0.2 - - - -
123V GLU* 1.3 75.4 - - - +
125V LYS* 1.3 57.1 + - - +
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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