Contacts of the helix formed by residues 103 - 118 (chain J) in PDB entry 5T0G
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 THR 103 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J VAL* 5.4 0.4 - - - -
94J HIS* 4.0 6.6 - - + -
100J ASP* 5.6 2.9 - - - +
101J PRO 4.3 8.3 - - - +
102J VAL* 1.3 77.8 - - - +
104J VAL* 1.3 65.7 - - - +
105J GLU* 4.2 9.6 + - - +
106J TYR* 3.0 30.1 + - - +
107J ILE* 3.1 14.8 + - - +
137J ASP* 4.9 5.2 - - - +
143J ARG* 3.6 11.0 - - - +
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Residues in contact with VAL 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J VAL* 5.1 2.8 - - + +
103J THR* 1.3 71.7 - - - +
105J GLU* 1.3 59.3 + - + +
107J ILE* 3.5 8.1 - - + -
108J THR* 2.5 56.5 + - + -
133J ILE* 4.0 18.6 - - + -
137J ASP* 4.8 3.4 - - - +
143J ARG* 3.4 48.4 - - + +
144J LEU* 4.4 2.5 - - - +
145J TYR* 3.5 35.4 - - + +
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Residues in contact with GLU 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J THR* 3.1 7.5 + - - +
104J VAL* 1.3 82.3 - - + +
106J TYR* 1.3 63.7 + - - +
108J THR* 3.8 1.7 + - - -
109J ARG* 3.1 72.8 + - + +
145J TYR* 3.9 31.2 - - + +
153J TYR* 4.6 9.9 + - + -
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Residues in contact with TYR 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J GLU* 2.8 31.1 + - + -
93J SER* 5.1 1.9 + - - -
94J HIS* 3.3 52.2 - + + +
102J VAL* 4.5 2.0 - - + -
103J THR* 3.0 21.8 + - - +
105J GLU* 1.3 82.1 + - - +
107J ILE* 1.3 67.2 + - + +
109J ARG* 3.5 30.6 + - - +
110J TYR* 3.3 17.0 + - - +
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Residues in contact with ILE 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65J LEU* 4.1 18.4 - - + -
69J VAL* 4.7 13.2 - - + -
71J MET* 5.4 4.7 - - + -
87J ALA 3.8 19.1 - - - +
90J GLU* 3.7 26.5 - - + -
91J CYS* 4.1 8.3 - - - +
102J VAL* 3.9 15.3 - - + -
103J THR 3.1 17.7 + - - +
104J VAL* 3.3 13.7 - - - +
106J TYR* 1.3 77.9 - - + +
108J THR* 1.3 74.2 + - + +
109J ARG 3.1 1.3 - - - -
110J TYR* 2.8 22.2 + - - +
111J ILE* 3.1 27.7 + - + +
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Residues in contact with THR 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104J VAL* 2.5 45.5 + - + +
105J GLU* 3.8 5.0 + - - -
107J ILE* 1.3 78.9 - - + +
109J ARG* 1.3 59.3 + - - +
111J ILE* 3.1 12.6 + - + +
112J ALA* 2.9 30.0 + - - +
133J ILE* 3.6 30.5 - - + -
145J TYR* 4.0 20.3 - - + +
146J GLN 5.2 3.1 - - - -
147J THR* 5.2 3.9 - - + +
153J TYR* 4.5 12.3 - - - +
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Residues in contact with ARG 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105J GLU* 3.1 50.5 + - - +
106J TYR* 3.5 34.4 - - - +
107J ILE 3.1 0.2 - - - -
108J THR* 1.3 80.3 + - - +
110J TYR* 1.3 57.0 + - - +
112J ALA* 4.0 6.1 - - - +
113J SER* 2.9 31.7 + - - -
153J TYR* 3.5 42.2 - - + -
90K ASP* 5.9 1.6 + - - -
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Residues in contact with TYR 110 (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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86J ARG* 3.5 44.2 + - + -
87J ALA* 4.9 0.7 - - - -
89J VAL* 6.0 1.2 - - - +
90J GLU* 3.2 57.5 + - + +
106J TYR 3.3 9.2 + - - +
107J ILE 2.8 13.1 + - - +
109J ARG* 1.3 76.0 - - - +
111J ILE* 1.3 76.2 + - + +
113J SER* 3.0 21.1 + - - -
114J LEU* 3.0 30.0 + - + +
117J ARG* 6.0 2.0 - - - -
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Residues in contact with ILE 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71J MET* 6.1 2.2 - - - -
83J VAL* 4.0 30.3 - - + +
86J ARG* 6.0 2.5 - - + -
87J ALA* 3.6 29.6 - - + +
107J ILE* 3.1 32.4 + - + +
108J THR* 3.1 9.2 + - - +
110J TYR* 1.3 85.7 - - + +
112J ALA* 1.3 60.0 + - - +
114J LEU* 3.9 3.6 - - - +
115J LYS* 2.9 35.3 + - + +
133J ILE* 5.9 4.5 - - + -
147J THR* 3.7 29.8 - - + -
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Residues in contact with ALA 112 (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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108J THR 2.9 15.9 + - - +
109J ARG* 4.0 6.7 - - - +
111J ILE* 1.3 78.3 - - + +
113J SER* 1.3 60.8 + - - +
115J LYS* 3.3 2.3 + - - -
116J GLN* 2.9 28.6 + - - +
147J THR* 5.8 5.4 - - + -
151J GLY* 3.2 40.2 - - - +
153J TYR* 4.4 18.4 - - + +
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Residues in contact with SER 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J ARG 2.9 17.0 + - - -
110J TYR* 3.0 18.0 + - - -
112J ALA* 1.3 76.1 - - - +
114J LEU* 1.3 71.2 + - - +
116J GLN* 2.9 17.9 + - - +
117J ARG* 3.0 36.1 + - - -
83K ALA* 6.5 0.2 - - - -
86K LYS* 6.1 6.3 - - - -
87K THR* 5.6 0.6 + - - -
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Residues in contact with LEU 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86J ARG* 3.7 40.6 - - + +
110J TYR* 3.0 44.7 + - + +
111J ILE* 4.1 3.6 - - - +
113J SER* 1.3 81.6 + - - +
115J LYS* 1.3 59.9 + - + +
117J ARG* 3.4 24.9 - - + +
118J TYR* 2.9 36.3 + - + +
124J ARG* 5.3 5.8 - - - +
127J PHE* 5.8 7.2 - - + -
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Residues in contact with LYS 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J ILE* 2.9 26.9 + - + +
112J ALA* 3.7 4.7 - - - +
113J SER 3.1 0.2 - - - -
114J LEU* 1.3 77.3 - - + +
116J GLN* 1.3 61.0 + - - +
118J TYR* 3.1 12.6 + - + +
119J THR* 2.9 33.1 + - + +
127J PHE* 4.1 40.1 + - + +
129J ILE* 2.6 31.7 + - - +
130J SER* 4.6 2.6 - - - +
147J THR* 5.2 4.8 + - - -
148J ASP 3.3 22.7 + - - +
149J PRO* 3.3 30.0 - - - +
150J SER 5.2 0.7 - - - -
151J GLY* 4.4 3.1 - - - +
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Residues in contact with GLN 116 (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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112J ALA 2.9 14.7 + - - +
113J SER* 2.9 12.5 + - - +
115J LYS* 1.3 74.4 - - - +
117J ARG* 1.3 60.3 + - - +
119J THR* 2.3 33.5 + - - -
120J GLN* 3.0 5.9 + - - +
150J SER* 2.7 35.4 + - - +
83K ALA* 3.4 28.6 - - + +
84K ASP* 3.1 24.5 + - - +
86K LYS* 6.3 0.2 - - + -
87K THR* 4.0 14.1 - - - +
135K ARG* 2.6 29.9 + - - +
137K PHE* 4.1 10.1 - - + -
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Residues in contact with ARG 117 (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 TYR* 6.0 2.6 - - - -
113J SER* 3.0 22.2 + - - -
114J LEU* 3.4 49.4 - - + +
116J GLN* 1.3 81.2 - - - +
118J TYR* 1.3 60.0 - - - +
119J THR 3.0 0.2 - - - -
120J GLN* 2.9 25.4 + - + -
121J SER* 3.1 21.1 + - - -
124J ARG* 4.9 0.5 - - - +
87K THR* 5.1 20.3 + - + +
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Residues in contact with TYR 118 (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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123I GLN* 3.2 31.7 - - + +
124I PHE* 6.1 1.3 - + - -
114J LEU* 2.9 25.8 + - + +
115J LYS* 3.1 13.7 - - + +
116J GLN 3.0 0.4 - - - -
117J ARG* 1.3 76.8 - - + +
119J THR* 1.3 56.2 + - - +
124J ARG* 3.0 75.9 - - + +
125J ARG 2.8 32.7 + - - -
126J PRO* 4.1 8.3 - - + -
127J PHE* 3.2 45.3 - + - -
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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