Contacts of the helix formed by residues 95 - 110 (chain J) in PDB entry 6LTJ
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 95 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43J MET* 5.7 1.9 - - - +
85J ILE* 4.5 15.5 - - + +
86J SER 5.2 0.7 - - - +
87J PRO* 3.3 15.1 + - + +
94J GLU* 1.3 75.4 - - + +
96J TRP* 1.3 57.6 + - - +
97J ASP* 3.3 14.3 + - - +
98J SER* 2.8 61.2 + - - +
99J PHE* 2.8 16.4 + - - +
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Residues in contact with TRP 96 (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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93J VAL* 3.6 28.3 - - + -
94J GLU 3.2 25.9 + - - -
95J ASP* 1.3 72.8 - - - +
97J ASP* 1.3 64.6 + - - +
99J PHE* 3.5 9.9 - + - +
100J GLN* 2.8 32.3 + - - +
132J LYS* 3.6 31.1 - - + +
135J LYS* 3.6 45.9 - - + +
136J LEU* 3.4 40.8 - - + -
139J LEU* 3.6 26.7 - - + +
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Residues in contact with ASP 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68J TYR* 5.9 7.0 - - + +
95J ASP* 3.1 11.5 - - - +
96J TRP* 1.3 83.5 - - - +
98J SER* 1.3 57.8 + - - +
100J GLN* 3.2 19.9 + - - +
101J ALA* 3.0 24.1 + - - +
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Residues in contact with SER 98 (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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41J ILE* 3.7 27.3 - - - +
68J TYR* 5.9 5.7 - - - -
85J ILE* 5.0 5.1 - - - +
87J PRO* 3.2 18.4 - - - +
95J ASP* 2.8 45.8 + - - +
97J ASP* 1.3 73.7 - - - +
99J PHE* 1.3 57.3 + - - +
101J ALA* 3.2 10.1 + - - +
102J ILE* 2.9 32.1 + - - +
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Residues in contact with PHE 99 (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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18J ILE* 3.6 44.6 - - + -
87J PRO* 4.3 16.6 - - + -
88J LEU* 4.6 1.3 - - + -
93J VAL* 4.2 26.0 - - + -
95J ASP 2.8 18.9 + - - +
96J TRP* 3.5 12.8 - + - +
97J ASP 3.2 0.4 - - - -
98J SER* 1.3 78.7 + - - +
100J GLN* 1.3 58.7 + - - +
102J ILE* 3.1 9.7 + - + +
103J LEU* 3.0 50.1 + - + +
122J MET* 5.0 8.7 - - + -
136J LEU* 4.0 24.2 - - + -
139J LEU* 4.4 15.7 - - + -
140J MET* 5.7 3.4 - - - -
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Residues in contact with GLN 100 (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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96J TRP 2.8 16.1 + - - +
97J ASP* 3.2 22.8 + - - +
99J PHE* 1.3 73.4 - - - +
101J ALA* 1.3 65.3 + - - +
103J LEU* 3.8 7.6 - - - -
104J ASP* 2.9 27.7 + - - +
139J LEU* 3.8 30.3 - - + -
143J HIS* 3.9 24.8 + - + +
144J TYR* 3.2 8.8 + - - +
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Residues in contact with ALA 101 (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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41J ILE* 5.3 3.8 - - + -
68J TYR* 5.4 12.6 - - + -
70J ILE* 4.6 14.1 - - + +
97J ASP 3.0 14.9 + - - +
98J SER* 3.2 14.6 + - - +
100J GLN* 1.3 83.0 - - - +
102J ILE* 1.3 57.6 + - - +
104J ASP* 3.4 8.1 + - - +
105J HIS* 2.9 28.3 + - - +
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Residues in contact with ILE 102 (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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18J ILE* 5.1 8.3 - - + -
23J VAL* 4.6 19.3 - - + -
37J PHE* 4.2 11.7 - - + -
39J THR* 5.4 8.1 - - - +
41J ILE* 3.7 23.3 - - + -
70J ILE* 3.4 37.2 - - + -
87J PRO* 4.6 7.0 - - + -
98J SER 2.9 17.2 + - - +
99J PHE* 3.1 14.3 + - + +
101J ALA* 1.3 75.0 - - - +
103J LEU* 1.3 65.4 + - + +
105J HIS* 3.2 1.9 + - - +
106J THR* 2.9 40.9 + - + +
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Residues in contact with LEU 103 (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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16J PHE* 4.3 18.4 - - + -
18J ILE* 5.0 7.0 - - + -
99J PHE* 3.0 51.1 + - + +
100J GLN* 3.7 6.1 - - - +
101J ALA 3.4 0.2 - - - -
102J ILE* 1.3 81.0 - - + +
104J ASP* 1.3 56.4 + - - +
106J THR* 2.5 19.3 + - - -
107J TYR* 3.0 42.6 + - + -
122J MET* 5.6 5.6 - - - -
139J LEU* 5.6 1.6 - - + -
140J MET* 4.6 20.9 - - + -
144J TYR* 3.3 27.1 - - + +
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Residues in contact with ASP 104 (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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100J GLN* 2.9 22.8 + - - +
101J ALA* 3.6 8.0 - - - +
103J LEU* 1.3 75.0 - - - +
105J HIS* 1.3 59.9 + - - +
107J TYR* 3.9 4.0 - - - +
108J LYS* 2.8 63.3 + - - +
144J TYR* 2.9 14.3 + - - +
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Residues in contact with HIS 105 (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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37J PHE* 4.2 14.6 - + - -
70J ILE* 4.1 36.3 - - + +
71J ASP* 3.3 29.8 + - - +
101J ALA 2.9 17.6 + - - +
102J ILE* 3.2 8.0 + - + +
104J ASP* 1.3 77.2 + - - +
106J THR* 1.3 59.6 + - - +
108J LYS* 5.4 0.2 - - - -
109J MET* 2.7 67.2 + - + +
110J HIS* 4.2 11.4 + + - -
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Residues in contact with THR 106 (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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16J PHE* 3.8 27.8 - - + -
23J VAL* 4.5 8.7 - - + -
25J ALA* 4.6 7.6 - - + -
35J VAL* 5.2 1.6 - - + -
37J PHE* 4.0 28.7 - - + -
102J ILE* 2.9 23.3 + - + +
103J LEU* 2.5 27.4 + - + -
105J HIS* 1.3 75.7 - - - +
107J TYR* 1.3 56.6 + - - -
110J HIS* 2.9 15.9 + - - +
111J VAL* 2.8 29.2 + - - +
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Residues in contact with TYR 107 (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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14J LEU* 5.0 5.4 - - + +
16J PHE* 3.6 27.6 - + - -
103J LEU* 3.0 39.6 + - + +
104J ASP* 3.9 5.2 - - - +
106J THR* 1.3 82.2 + - - +
108J LYS* 1.3 61.3 + - + +
111J VAL* 3.4 13.2 - - + +
112J LYS 3.2 21.3 + - - -
113J SER 2.9 20.8 - - - +
114J GLU* 4.5 2.9 - - - -
115J ALA* 3.2 46.7 - - + -
118J HIS* 5.6 2.7 - + - +
120J VAL* 3.6 21.0 - - - +
140J MET* 5.9 0.7 - - + -
144J TYR* 5.1 10.1 - + + -
146J ILE* 3.3 30.4 - - + +
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Residues in contact with LYS 108 (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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104J ASP* 2.8 52.0 + - - +
105J HIS* 5.4 0.4 - - - -
107J TYR* 1.3 77.0 - - + +
109J MET* 1.3 71.3 + - + +
112J LYS* 4.4 12.9 - - - +
113J SER 4.4 4.0 - - - +
114J GLU* 3.8 39.3 - - + +
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Residues in contact with MET 109 (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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71J ASP* 5.7 2.0 - - - +
105J HIS* 2.7 45.5 + - + +
107J TYR 3.1 0.4 - - - -
108J LYS* 1.3 89.3 - - + +
110J HIS* 1.3 83.3 + - + +
111J VAL 3.9 0.2 - - - -
112J LYS* 3.7 21.5 - - - +
177K ARG* 3.5 34.1 - - - +
179K ASP* 4.5 13.5 - - + +
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Residues in contact with HIS 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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34J LYS* 3.8 18.9 + - - -
35J VAL* 3.7 41.6 - - + +
37J PHE* 4.7 10.3 - + - -
71J ASP* 5.0 6.7 + - - +
105J HIS* 4.2 21.5 + + - -
106J THR* 2.9 10.2 + - - +
109J MET* 1.3 96.3 + - + +
111J VAL* 1.3 65.3 + - - +
112J LYS* 3.4 1.8 - - - +
110K LEU* 4.4 17.9 - - + +
175K ILE 6.1 1.1 - - - -
176K LEU* 6.0 5.8 - - + -
177K ARG* 3.9 27.8 - - + -
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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