Contacts of the helix formed by residues 107 - 121 (chain R) in PDB entry 5G04
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 PRO 107 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108R THR* 1.3 69.7 + - + +
109R LYS* 3.3 29.2 - - + -
110R LYS* 3.2 26.2 + - + +
111R GLU* 2.9 26.3 + - - +
434R ALA* 6.5 2.0 - - + -
435R LYS* 5.9 13.2 - - + +
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Residues in contact with THR 108 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107R PRO* 1.3 86.1 - - + +
109R LYS* 1.3 58.6 + - - +
111R GLU* 3.0 8.9 + - - +
112R HIS* 3.0 27.5 + - - +
435R LYS* 3.9 25.6 - - + +
436R VAL 5.6 3.6 - - - +
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Residues in contact with LYS 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199A LYS 5.7 0.7 - - - +
107R PRO* 3.4 29.6 - - + -
108R THR* 1.3 81.2 + - - +
110R LYS* 1.3 72.9 + - - +
112R HIS* 3.6 9.5 - - - +
113R GLN* 3.4 26.3 + - - +
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Residues in contact with LYS 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107R PRO* 3.2 24.0 + - + +
108R THR 3.2 0.4 - - - -
109R LYS* 1.3 90.9 - - + +
111R GLU* 1.3 76.3 + - + +
113R GLN* 3.1 23.8 + - - +
114R LYS* 3.0 48.0 + - - +
126R GLU* 3.2 28.0 + - - +
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Residues in contact with GLU 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107R PRO 2.9 15.1 + - - +
108R THR* 3.0 10.6 + - - +
110R LYS* 1.3 95.7 - - + +
112R HIS* 1.3 56.0 + - - +
114R LYS* 3.8 24.3 + - - +
115R ALA* 2.8 38.8 + - - +
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Residues in contact with HIS 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1198A THR* 3.2 25.4 + - - -
1200A GLY* 3.3 28.0 + - - -
1244A ASP* 5.1 4.8 + - - -
1246A PRO* 5.4 12.6 - - + -
108R THR 3.0 11.6 + - - +
109R LYS* 3.6 14.1 - - - +
111R GLU* 1.3 72.2 - - - +
113R GLN* 1.3 66.4 + - + +
115R ALA* 2.9 17.3 + - - +
116R TRP* 3.0 49.5 + + - -
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Residues in contact with GLN 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1198A THR* 3.4 34.7 + - - +
1199A LYS* 4.9 24.6 + - - +
97R LYS* 5.8 3.8 + - - -
109R LYS* 3.4 15.4 + - - +
110R LYS* 3.1 27.2 + - - +
112R HIS* 1.3 76.7 - - - +
114R LYS* 1.3 51.8 + - - +
116R TRP 2.9 6.1 + - - -
117R ALA* 2.7 32.0 + - + -
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Residues in contact with LYS 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110R LYS* 3.0 39.6 + - - +
111R GLU* 3.8 19.9 + - - +
112R HIS 3.3 0.2 - - - -
113R GLN* 1.3 75.5 - - - +
115R ALA* 1.3 68.4 + - - +
117R ALA* 3.9 8.1 - - + -
118R LEU* 2.9 61.7 + - + +
124R ASP* 3.9 25.8 + - - -
126R GLU* 3.4 14.6 + - - +
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Residues in contact with ALA 115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1242A GLU* 5.4 4.5 - - - +
1244A ASP* 5.0 7.2 - - - +
111R GLU* 2.8 23.8 + - - +
112R HIS* 3.2 6.5 - - - +
114R LYS* 1.3 77.8 - - - +
116R TRP* 1.3 69.4 + - + +
118R LEU* 4.1 1.7 - - - +
119R ASN* 2.9 41.7 + - - +
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Residues in contact with TRP 116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197A LEU 3.5 22.0 - - - +
1198A THR* 3.5 10.8 - - + -
1230A ILE* 4.6 17.5 - - + +
1231A HIS* 4.9 10.8 + + - -
1242A GLU 4.9 0.2 - - - -
1243A LEU* 3.9 2.7 - - - +
1244A ASP* 3.3 63.3 - - - -
1245A VAL* 3.7 23.3 - - + +
1246A PRO* 5.1 2.0 - - + -
112R HIS* 3.0 62.4 + + - -
113R GLN 2.9 3.9 + - - +
115R ALA* 1.3 78.7 - - + +
117R ALA* 1.3 58.4 + - - +
119R ASN* 3.9 23.2 - - + +
120R LEU* 2.9 36.6 + - + +
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Residues in contact with ALA 117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1194A HIS 5.0 2.9 - - - +
1198A THR* 3.3 10.9 - - + +
97R LYS* 5.9 5.2 - - - +
113R GLN* 2.7 21.0 + - + +
114R LYS* 3.9 10.1 - - + -
116R TRP* 1.3 70.9 - - - +
118R LEU* 1.3 60.3 + - - +
120R LEU* 3.3 3.5 + - - +
121R ASN* 3.1 36.2 + - - +
124R ASP* 5.7 1.3 - - - -
125R VAL* 5.2 13.2 - - + +
126R GLU* 4.7 10.3 - - - +
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Residues in contact with LEU 118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1241A THR* 6.3 4.7 - - + -
114R LYS* 2.9 50.4 + - + +
115R ALA* 4.2 2.5 - - - +
117R ALA* 1.3 74.2 - - - +
119R ASN* 1.3 61.3 + - - +
121R ASN 3.0 17.3 - - - +
122R GLY* 3.6 21.9 - - - +
124R ASP* 4.2 19.7 - - + +
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Residues in contact with ASN 119 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1226A ARG* 5.7 2.6 - - - +
1230A ILE* 3.2 36.9 - - + +
1239A THR* 4.9 5.5 - - - +
1241A THR* 2.7 47.8 + - - +
1242A GLU 4.7 7.1 + - - -
1243A LEU* 4.7 1.8 - - - +
115R ALA* 2.9 31.1 + - - +
116R TRP* 3.7 21.4 - - + +
117R ALA 3.2 0.4 - - - -
118R LEU* 1.3 80.8 - - - +
120R LEU* 1.3 62.7 + - - +
121R ASN 4.6 1.2 - - - -
122R GLY* 4.9 0.9 + - - -
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Residues in contact with LEU 120 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1194A HIS* 3.6 50.1 - - + +
1197A LEU* 3.3 35.7 - - + +
1226A ARG* 4.4 21.2 + - - +
1227A LEU* 3.7 43.4 + - + -
1230A ILE* 3.9 18.8 - - + -
1231A HIS* 4.6 1.3 - - + -
116R TRP* 2.9 23.3 + - + +
117R ALA 3.3 2.6 + - - +
119R ASN* 1.3 78.3 - - - +
121R ASN* 1.3 58.6 + - - +
122R GLY 4.4 0.2 + - - -
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Residues in contact with ASN 121 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1191A LEU* 3.6 33.6 - - + +
1194A HIS* 4.2 20.7 + - + +
117R ALA* 3.1 16.0 + - - +
118R LEU* 3.0 16.4 - - - +
120R LEU* 1.3 77.1 - - - +
122R GLY* 1.3 65.3 + - - +
123R PHE* 3.5 25.5 - - + +
124R ASP 3.9 3.5 + - - -
125R VAL* 3.7 19.1 - - - +
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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