Contacts of the helix formed by residues 108 - 121 (chain B) in PDB entry 1JAT
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 108 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ARG* 3.6 24.2 - - - +
13B GLU* 3.3 17.5 - - + -
68B TYR* 3.7 3.1 - - - -
103B TRP* 3.9 9.6 - - - -
106B ALA 3.8 9.6 - - - +
107B TYR* 1.3 77.7 - - - +
109B MET* 1.3 64.9 + - - +
110B GLU* 3.3 20.6 + - - +
111B THR* 3.0 26.9 + - - +
112B LEU* 3.2 9.7 + - - +
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Residues in contact with MET 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.2 6.5 - - + -
13B GLU* 2.9 33.7 + - + +
28B TYR* 4.2 14.8 - - + -
41B TRP* 3.5 62.1 - - + +
62B ILE* 3.9 33.4 - - + -
64B CYS* 3.8 12.1 - - - -
68B TYR* 3.5 10.4 + - + +
73B PRO* 5.2 2.5 - - + -
103B TRP* 5.4 0.4 - - - -
108B THR* 1.3 72.5 - - - +
110B GLU* 1.3 57.0 + - - +
112B LEU* 3.4 8.6 + - - +
113B LEU* 3.0 34.5 + - - +
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLU* 4.4 0.4 + - - -
16B LYS* 2.8 41.4 + - - +
26B CYS* 6.4 0.9 - - + -
28B TYR* 4.4 21.4 - - + +
108B THR* 3.0 11.9 + - - +
109B MET* 1.3 79.0 - - - +
111B THR* 1.3 62.9 + - - +
113B LEU* 3.3 5.6 + - - +
114B LEU* 2.9 50.6 + - + +
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Residues in contact with THR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B THR* 4.3 5.2 - - + -
106B ALA 4.9 0.3 + - - -
107B TYR* 3.8 30.5 - - + -
108B THR* 3.0 31.6 + - - +
110B GLU* 1.3 79.6 - - - +
112B LEU* 1.3 56.9 + - - +
114B LEU* 3.7 6.8 - - - +
115B ASP* 2.9 51.4 + - - +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ILE* 5.3 3.1 - - + -
73B PRO* 3.6 23.8 - - + -
75B VAL* 3.1 36.6 - - + -
93B VAL* 5.8 0.7 - - + -
97B PHE* 4.2 11.9 - - + -
99B THR* 3.9 29.6 - - + +
100B LEU* 3.9 20.2 - - + -
103B TRP* 4.5 5.4 - - + -
108B THR 3.2 7.9 + - - +
109B MET* 3.7 10.1 - - - +
110B GLU 3.3 0.2 - - - -
111B THR* 1.3 77.8 - - - +
113B LEU* 1.3 62.6 + - + +
115B ASP* 3.3 2.2 + - - +
116B LEU* 2.9 43.0 + - + +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B CYS* 3.8 24.4 - - + -
27B SER 3.5 25.1 - - - +
28B TYR* 4.0 22.4 - - + -
43B GLY* 4.6 2.9 - - - -
44B THR 4.5 0.9 - - - +
45B ILE* 3.8 28.5 - - + +
60B LEU* 4.2 20.0 - - + -
62B ILE* 4.4 18.4 - - + -
75B VAL* 5.6 1.1 - - + -
109B MET 3.0 21.1 + - - +
110B GLU* 3.9 4.9 - - - +
112B LEU* 1.3 76.4 - - + +
114B LEU* 1.3 57.5 + - - +
116B LEU* 3.4 5.5 + - + +
117B ARG* 3.0 27.9 + - - +
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B SER* 4.0 11.2 - - - +
26B CYS* 3.7 25.6 - - + +
110B GLU* 2.9 46.3 + - + +
111B THR* 3.7 6.1 - - - +
113B LEU* 1.3 76.2 - - - +
115B ASP* 1.3 62.3 + - - +
117B ARG* 3.3 6.8 + - - +
118B LYS* 3.0 33.4 + - + +
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Residues in contact with ASP 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PHE* 3.7 9.6 - - + -
98B HIS* 3.7 19.4 + - - +
99B THR* 2.5 38.6 + - - +
111B THR* 2.9 25.9 + - - +
112B LEU 3.7 3.8 - - - +
114B LEU* 1.3 77.7 - - - +
116B LEU* 1.3 60.0 + - - +
118B LYS* 3.4 10.3 + - - +
119B GLU* 3.0 26.5 + - - +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 3.8 10.5 - - + -
60B LEU* 4.0 28.0 - - + -
75B VAL* 4.2 13.2 - - + -
77B PHE* 4.2 13.5 - - + -
83B LEU* 4.6 3.6 - - + +
85B CYS* 4.1 20.0 - - - -
93B VAL* 4.2 15.3 - - + -
97B PHE* 3.7 26.7 - - + -
112B LEU* 2.9 31.0 + - + +
113B LEU* 3.7 6.3 - - + +
115B ASP* 1.3 73.0 - - - +
117B ARG* 1.3 66.1 + - - +
119B GLU* 3.2 4.7 + - - +
120B MET* 3.1 27.1 + - - +
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Residues in contact with ARG 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B SER* 3.1 38.2 + - - -
26B CYS* 4.2 2.9 - - - -
45B ILE* 3.8 13.0 - - + +
46B LEU* 2.8 32.8 + - - +
47B GLY 3.7 6.1 + - - -
48B PRO* 3.6 38.3 - - + +
49B PRO* 3.8 12.1 - - - +
113B LEU 3.0 14.2 + - - +
114B LEU* 3.6 10.1 - - - +
115B ASP 3.3 0.2 - - - -
116B LEU* 1.3 76.4 - - - +
118B LYS* 1.3 64.3 + - - +
120B MET* 3.1 25.4 + - - +
121B ALA* 3.6 4.2 + - - +
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU* 3.0 17.4 + - + +
115B ASP* 3.5 15.0 - - - +
117B ARG* 1.3 78.4 - - + +
119B GLU* 1.3 61.2 + - - +
121B ALA* 3.0 22.4 + - + +
122B THR* 3.7 8.0 + - - +
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Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 4.2 7.4 - - + -
84B PRO* 5.2 2.6 - - + +
85B CYS* 4.2 16.2 - - + -
97B PHE* 3.8 28.0 - - + -
98B HIS* 4.6 8.8 + - - -
115B ASP 3.0 13.4 + - - +
116B LEU* 3.2 10.5 + - - +
118B LYS* 1.3 76.0 - - - +
120B MET* 1.3 62.1 + - - +
121B ALA 3.1 0.9 + - - -
122B THR* 3.4 23.4 + - - +
125B ASN* 2.7 48.6 - - - +
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Residues in contact with MET 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 3.8 32.1 - - + -
47B GLY* 4.5 0.2 - - - -
48B PRO* 3.7 24.8 - - + +
51B SER* 4.3 0.5 - - - -
53B HIS* 3.3 34.5 + - + +
58B TYR* 3.9 23.8 - - + -
77B PHE* 4.0 18.8 - - + -
81B ILE* 3.7 20.4 - - + -
83B LEU* 4.1 18.8 - - + -
116B LEU 3.1 14.5 + - - +
117B ARG* 3.1 9.8 + - - +
119B GLU* 1.3 76.0 - - - +
121B ALA* 1.3 56.8 + - - +
122B THR 3.6 0.4 - - - -
125B ASN* 4.0 1.2 - - - -
126B LYS* 3.7 15.9 + - - +
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PRO* 3.9 23.6 - - + -
49B PRO 5.2 4.7 - - - +
51B SER* 5.0 1.6 - - - -
117B ARG 3.6 2.2 + - - +
118B LYS* 3.0 16.7 + - + +
120B MET* 1.3 79.4 - - - +
122B THR* 1.3 63.8 + - - +
123B PRO* 3.6 2.4 - - - +
126B LYS* 3.8 18.0 + - - +
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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