Contacts of the helix formed by residues 121 - 138 (chain J) in PDB entry 5JGH
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 GLY 121 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119J PRO 3.6 2.2 + - - -
120J ALA* 1.3 77.4 - - - +
122J PRO* 1.3 80.2 - - - +
123J PHE 3.3 2.5 - - - -
124J ILE* 3.2 18.6 + - - +
125J LYS* 3.3 8.1 + - - +
169J TYR* 3.6 10.1 - - - -
4K A 6.1 0.4 - - - -
5K T 5.0 8.3 - - - -
6K T 5.5 0.7 - - - -
18L A 6.4 0.2 - - - -
19L T 4.3 12.5 + - - -
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Residues in contact with PRO 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J GLY* 1.3 84.0 - - - +
123J PHE* 1.3 64.2 + - - +
125J LYS* 3.3 7.2 + - + +
126J TYR* 3.1 17.3 + - - +
154J TRP* 4.0 11.7 - - + -
165J TYR* 3.9 32.0 - - + +
166J ILE* 4.0 7.2 - - + +
169J TYR* 3.6 28.9 - - + -
5K T 3.6 33.9 - - - +
6K T 3.8 15.5 - - - +
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Residues in contact with PHE 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J GLY 3.3 1.0 - - - -
122J PRO* 1.3 79.2 - - - +
124J ILE* 1.3 64.3 + - + +
126J TYR* 3.1 3.4 + + - +
127J ALA* 2.7 42.0 + - + +
147J MET* 4.4 3.8 - - - -
150J ILE* 3.8 32.8 - - + -
151J GLY* 3.8 16.4 - - - -
154J TRP* 3.5 48.2 - + + -
3K T 3.5 39.3 - - + -
4K A 3.1 38.4 - - - +
5K T 4.5 5.3 + - - +
20L A 5.9 0.2 - + - -
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Residues in contact with ILE 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J ALA* 3.7 14.8 - - + -
121J GLY 3.2 13.1 + - - +
123J PHE* 1.3 81.2 - - + +
125J LYS* 1.3 59.3 + - - +
127J ALA* 2.9 6.4 + - - +
128J ASN* 2.6 53.5 + - - +
131J ARG* 5.0 0.2 - - - +
3K T 5.3 0.9 - - - +
4K A 3.5 24.2 - - + +
19L T 3.2 29.4 - - + +
20L A 3.3 50.9 - - + +
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Residues in contact with LYS 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J PRO* 6.0 1.8 - - - -
120J ALA* 4.0 31.4 - - + +
121J GLY 3.3 9.8 + - - +
122J PRO* 3.3 11.5 + - + +
124J ILE* 1.3 77.5 - - - +
126J TYR* 1.3 62.8 + - - +
128J ASN* 3.4 14.4 + - + +
129J GLU* 3.0 29.7 + - + +
165J TYR* 3.9 16.6 - - + +
168J GLU* 4.1 21.5 - - + +
169J TYR* 6.4 2.2 - - + -
20L A 6.1 1.2 - - - -
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Residues in contact with TYR 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122J PRO 3.1 2.2 + - - +
123J PHE* 3.1 9.2 + + - +
125J LYS* 1.3 78.3 - - - +
127J ALA* 1.3 66.1 + - - +
129J GLU* 3.0 12.7 + - + +
130J VAL* 3.1 29.9 + - + +
150J ILE* 3.8 24.5 - - + -
153J LYS* 3.1 36.8 + - + +
154J TRP* 3.7 48.0 - + + -
157J LEU* 3.8 28.2 - - + +
161J ILE* 5.3 1.6 - - + -
165J TYR* 3.5 36.9 - + + -
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Residues in contact with ALA 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123J PHE* 2.7 28.9 + - + +
124J ILE* 3.4 12.1 - - + +
126J TYR* 1.3 73.3 - - - +
128J ASN* 1.3 63.8 + - - +
130J VAL* 3.0 2.8 + - - +
131J ARG* 2.9 36.1 + - - +
147J MET* 4.4 14.8 - - + -
150J ILE* 3.9 27.4 - - + -
20L A 6.2 0.2 - - + -
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Residues in contact with ASN 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120J ALA* 5.4 0.2 - - - +
124J ILE* 2.6 38.2 + - - +
125J LYS* 3.8 17.1 - - + +
127J ALA* 1.3 71.7 - - - +
129J GLU* 1.3 63.5 + - + +
130J VAL 3.4 0.2 + - - -
131J ARG* 2.5 56.7 + - - +
132J SER* 5.1 1.0 + - - -
20L A 3.5 21.5 + - - +
21L A 3.8 11.7 + - - +
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Residues in contact with GLU 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J LYS* 3.0 12.1 + - + +
126J TYR* 3.0 8.1 + - + +
128J ASN* 1.3 78.0 - - + +
130J VAL* 1.3 59.9 + - + +
132J SER* 4.4 8.8 + - - -
133J GLN* 6.0 0.2 - - - +
165J TYR* 2.3 46.4 + - - +
168J GLU* 4.2 13.2 - - - +
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Residues in contact with VAL 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126J TYR* 3.1 35.5 + - + +
127J ALA* 3.0 14.8 + - - +
129J GLU* 1.3 77.6 - - + +
131J ARG* 1.3 65.9 + - - +
132J SER 3.4 2.5 - - - -
133J GLN* 3.4 17.7 + - + +
134J VAL* 3.2 33.3 + - + +
150J ILE* 3.9 21.5 - - + -
153J LYS* 4.0 13.7 - - - +
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Residues in contact with ARG 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124J ILE* 5.0 0.2 - - - +
127J ALA* 2.9 14.1 + - - +
128J ASN* 2.5 53.6 + - - +
129J GLU 3.6 1.6 - - - -
130J VAL* 1.3 77.1 - - - +
132J SER* 1.3 64.5 + - - +
134J VAL* 3.3 3.0 + - + +
135J PHE* 2.8 27.2 + - - +
143J GLN* 2.9 29.7 + - - -
146J LEU* 5.5 5.1 - - + +
147J MET* 3.2 25.0 - - + +
150J ILE* 3.8 21.5 - - + -
20L A 3.9 8.3 + - - -
21L A 3.1 36.4 + - - -
22L A 4.8 8.3 - - - -
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Residues in contact with SER 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J ASN 5.1 1.0 + - - -
129J GLU 4.4 9.9 + - - -
131J ARG* 1.3 78.1 - - - +
133J GLN* 1.3 68.0 + - - +
135J PHE* 3.4 7.8 + - - +
136J ALA* 3.0 23.6 + - - +
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Residues in contact with GLN 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J VAL* 3.4 18.0 + - + +
131J ARG 3.3 0.4 - - - -
132J SER* 1.3 82.5 + - - +
134J VAL* 1.3 60.9 + - + +
136J ALA* 3.1 8.7 + - - +
137J GLN* 2.9 54.9 + - + +
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Residues in contact with VAL 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J VAL* 3.2 31.4 + - + +
131J ARG* 3.5 9.0 - - + +
133J GLN* 1.3 77.8 - - + +
135J PHE* 1.3 60.6 + - - +
137J GLN* 3.1 15.8 + - - +
138J HIS* 2.7 40.2 + - + +
146J LEU* 4.3 15.5 - - + +
149J ILE* 5.3 4.0 - - + -
150J ILE* 3.6 28.9 - - + -
153J LYS* 3.8 25.8 - - + +
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Residues in contact with PHE 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J ARG 2.8 19.4 + - - +
132J SER* 3.7 7.0 - - - +
134J VAL* 1.3 75.5 - - - +
136J ALA* 1.3 67.1 + - - +
138J HIS 3.0 24.8 - - - +
139J PRO* 3.0 37.4 - - + +
141J LYS 4.1 8.5 - - - -
146J LEU* 3.5 28.0 - - + -
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Residues in contact with ALA 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J SER 3.0 13.7 + - - +
133J GLN* 3.3 11.7 - - - +
135J PHE* 1.3 78.6 - - - +
137J GLN* 1.3 62.9 + - + +
139J PRO* 3.5 13.0 - - - +
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Residues in contact with GLN 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J GLN* 2.9 42.3 + - + +
134J VAL* 3.4 26.3 + - - +
135J PHE 3.1 0.2 - - - -
136J ALA* 1.3 78.9 - - + +
138J HIS* 1.3 77.1 + - + +
139J PRO* 3.4 6.4 - - - +
153J LYS* 5.4 4.0 + - - +
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Residues in contact with HIS 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A GLN 5.0 5.4 + - - -
156A SER* 5.1 6.9 + - - -
134J VAL* 2.7 24.4 + - + +
135J PHE* 3.0 14.4 - - - +
137J GLN* 1.3 89.6 - - + +
139J PRO* 1.3 67.2 - - - +
140J ASP* 3.1 8.3 + - - -
141J LYS* 3.3 26.5 + - + -
146J LEU* 3.8 14.9 - - + +
149J ILE* 3.6 40.9 - - + +
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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