Contacts of the helix formed by residues 121 - 136 (chain J) in PDB entry 5GAG
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 121 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120J ALA* 1.3 92.4 - - - +
122J ILE* 1.3 64.4 + - - +
123J GLU* 3.0 32.0 - - + +
124J ALA* 3.1 14.9 + - + +
125J MET* 3.4 18.8 + - - +
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Residues in contact with ILE 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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107J GLN* 4.2 13.5 - - + +
110J ALA 4.2 13.2 - - - +
111J GLN* 3.6 38.1 - - + +
114J ALA* 6.0 1.6 - - + -
121J ASP* 1.3 72.4 - - - +
123J GLU* 1.3 61.6 + - - +
125J MET* 4.1 10.5 - - - -
126J THR* 2.9 47.0 + - - +
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Residues in contact with GLU 123 (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 ASP* 3.3 25.8 - - + +
122J ILE* 1.3 80.3 + - - +
124J ALA* 1.3 58.5 + - - +
126J THR* 3.8 3.3 - - - -
127J ARG* 2.9 54.7 + - - +
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Residues in contact with ALA 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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1080A A 3.7 3.5 + - - -
1081A U 3.4 41.7 - - - +
1082A U 4.3 3.6 - - - +
119J GLY* 3.7 3.8 - - - -
120J ALA* 3.6 16.6 - - + +
121J ASP* 3.1 14.1 + - - +
123J GLU* 1.3 78.3 - - - +
125J MET* 1.3 56.9 + - - +
127J ARG* 3.4 7.1 + - - +
128J SER* 3.0 27.8 + - - -
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Residues in contact with MET 125 (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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110J ALA* 3.3 20.9 - - + +
114J ALA* 3.5 39.3 - - + +
117J MET* 3.4 33.7 - - + +
119J GLY* 3.1 42.0 - - - +
120J ALA 4.7 2.2 - - - +
121J ASP 3.4 15.7 + - - +
122J ILE* 4.1 11.4 - - - +
124J ALA* 1.3 75.8 - - - +
126J THR* 1.3 56.9 + - - +
128J SER 3.4 0.5 + - - -
129J ILE* 3.0 34.7 + - - +
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Residues in contact with THR 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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103J ARG* 4.9 2.5 - - + +
106J LEU* 3.2 40.2 + - + +
107J GLN* 3.3 29.1 - - + +
110J ALA* 3.5 7.2 - - - +
122J ILE* 2.9 24.6 + - - +
123J GLU* 4.0 4.9 - - - +
125J MET* 1.3 75.9 - - - +
127J ARG* 1.3 57.2 + - - +
129J ILE* 3.8 1.7 - - - +
130J GLU* 2.9 38.8 + - - +
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Residues in contact with ARG 127 (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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1080A A 3.2 37.1 + - - +
1081A U 3.6 19.6 + - - -
123J GLU* 2.9 42.8 + - - +
124J ALA* 3.7 5.9 - - - +
126J THR* 1.3 76.4 - - - +
128J SER* 1.3 57.9 + - - +
130J GLU* 3.1 29.0 - - - +
131J GLY 3.0 19.4 + - - -
134J ARG* 4.0 0.2 + - - -
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Residues in contact with SER 128 (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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1058A U 4.5 0.5 + - - -
1059A G 2.7 31.8 + - - +
1080A A 2.8 37.2 + - - -
1081A U 3.6 7.5 + - - -
117J MET* 3.5 28.9 - - - -
124J ALA 3.0 13.8 + - - -
125J MET 3.4 0.4 + - - -
127J ARG* 1.3 72.3 - - - +
129J ILE* 1.3 61.3 + - - +
130J GLU 3.2 1.3 - - - -
131J GLY 3.2 0.2 + - - -
132J THR* 3.0 16.3 + - - -
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Residues in contact with ILE 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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1059A G 3.4 8.5 - - - +
76J ALA* 3.3 23.8 - - + -
80J LEU* 3.3 23.5 - - + +
106J LEU* 3.7 12.2 - - + +
109J ILE* 3.6 24.0 - - + -
110J ALA* 3.8 12.8 - - + -
113J LYS* 3.4 28.9 - - + -
117J MET* 3.5 5.6 - - + -
125J MET 3.0 18.4 + - - +
126J THR 3.8 3.1 - - - +
128J SER* 1.3 72.8 - - - +
130J GLU* 1.3 59.8 + - - +
131J GLY 3.3 0.2 - - - -
132J THR* 3.8 4.9 - - - +
133J ALA* 2.9 27.2 + - - +
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Residues in contact with GLU 130 (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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1080A A 5.6 0.7 - - - +
106J LEU* 3.8 20.0 - - + +
126J THR* 2.9 35.4 + - - +
127J ARG* 3.1 37.6 - - - +
129J ILE* 1.3 77.2 - - - +
131J GLY* 1.3 54.3 + - - +
133J ALA* 3.2 9.4 + - - +
134J ARG* 2.9 63.5 + - - +
140J VAL* 4.7 5.8 - - + +
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Residues in contact with GLY 131 (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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1059A G 3.7 0.9 - - - -
1079A C 2.9 35.4 - - - +
1088A A 3.0 17.1 + - - +
127J ARG 3.0 12.7 + - - -
128J SER 3.2 3.7 + - - -
130J GLU* 1.3 75.6 - - - +
132J THR* 1.3 56.3 + - - +
133J ALA 3.2 1.8 - - - -
134J ARG* 3.4 3.5 + - - +
135J SER* 2.9 21.8 + - - -
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Residues in contact with THR 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059A G 3.8 1.7 + - - -
1060A U 2.4 37.2 + - + +
1062A G 3.1 23.8 - - - +
1088A A 3.7 0.4 - - - +
76J ALA* 3.4 19.1 - - + +
77J ALA* 3.4 27.8 - - - +
80J LEU* 3.8 1.6 - - - -
128J SER 3.0 14.6 + - - -
129J ILE 3.6 3.1 + - - -
131J GLY* 1.3 73.2 - - - +
133J ALA* 1.3 57.4 + - - +
135J SER* 3.2 8.9 + - - -
136J MET* 3.0 24.1 - - - +
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Residues in contact with ALA 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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80J LEU* 3.6 6.7 - - + -
101J ILE* 3.4 31.6 - - + -
106J LEU* 4.1 0.2 - - + -
129J ILE 2.9 18.1 + - - +
130J GLU* 3.2 8.5 - - - +
131J GLY 3.2 0.4 - - - -
132J THR* 1.3 79.0 - - - +
134J ARG* 1.3 59.6 + - - +
135J SER 3.4 0.2 - - - -
136J MET* 4.1 2.4 + - - -
137J GLY 3.5 1.4 + - - -
138J LEU* 2.8 39.1 + - - +
140J VAL* 3.9 9.6 - - + -
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Residues in contact with ARG 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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1077A A 3.0 10.1 + - - +
1078A U 6.4 1.1 - - - -
1079A C 2.9 36.7 + - - +
1080A A 4.6 6.5 + - - -
93J PRO* 4.0 0.5 - - - +
94J ASN* 2.8 44.1 - - - +
127J ARG 4.0 3.0 + - - -
130J GLU* 2.9 66.1 + - - +
131J GLY* 3.5 5.3 - - - +
133J ALA* 1.3 78.4 - - + +
135J SER* 1.3 59.7 + - - +
136J MET 3.5 0.2 - - - -
137J GLY 3.6 4.5 + - - -
138J LEU 4.7 1.8 - - - +
140J VAL* 5.3 14.1 - - + +
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Residues in contact with SER 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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1062A G 2.7 65.9 + - - +
1063A G 4.0 0.9 - - - -
1077A A 4.2 6.3 - - - -
1088A A 3.1 39.1 + - - -
93J PRO* 3.0 6.8 - - - +
131J GLY 2.9 4.4 + - - -
132J THR* 3.2 13.3 + - - -
133J ALA 3.4 0.4 - - - -
134J ARG* 1.3 78.1 - - - +
136J MET* 1.3 58.8 + - - +
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Residues in contact with MET 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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1063A G 3.3 33.0 - - - +
77J ALA* 3.3 28.9 - - - +
80J LEU* 4.3 3.1 - - - -
81J LYS* 3.5 30.3 - - + -
86J ILE* 3.6 10.5 - - + -
89J GLY* 3.6 20.5 - - - +
90J SER* 2.6 30.6 + - - -
93J PRO* 3.9 5.8 - - - -
98J VAL* 3.8 2.6 - - - +
132J THR 3.0 20.2 - - - +
133J ALA 4.2 1.6 - - - +
135J SER* 1.3 76.1 + - - +
137J GLY* 1.3 58.9 + - - +
138J LEU* 3.6 20.9 + - + -
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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