Contacts of the helix formed by residues 91 - 105 (chain B) in PDB entry 1JQE
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 SER 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B GLU* 2.9 18.2 + - - +
90B PRO* 1.3 76.8 - - - +
92B ALA* 1.3 62.3 + - - +
93B GLU* 3.3 10.4 + - - +
94B GLN* 3.0 31.4 + - - +
95B ILE* 3.1 27.1 + - - +
401B SAH 3.7 6.7 - - - -
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Residues in contact with ALA 92 (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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90B PRO 3.5 5.3 + - - -
91B SER* 1.3 72.7 - - - +
93B GLU* 1.3 57.0 + - - +
95B ILE* 3.4 6.3 + - - +
96B ALA* 3.0 28.2 + - - +
117B LYS* 3.8 27.6 - - + +
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Residues in contact with GLU 93 (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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91B SER* 3.1 7.8 + - - +
92B ALA* 1.3 77.1 - - - +
94B GLN* 1.3 65.4 + - + +
96B ALA* 3.3 6.7 + - - +
97B LYS* 3.1 33.6 + - + +
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Residues in contact with GLN 94 (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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16B VAL* 5.7 5.7 - - - -
62B GLY* 3.4 29.1 - - - +
63B ALA* 3.8 9.3 + - - +
89B GLU* 3.8 6.7 - - + -
91B SER* 3.0 32.5 + - - +
93B GLU* 1.3 75.8 - - + +
95B ILE* 1.3 59.6 + - - +
97B LYS* 3.1 24.9 + - - +
98B TYR* 2.8 28.2 + - - +
401B SAH 2.8 35.6 + - - +
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Residues in contact with ILE 95 (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 GLY 4.7 0.9 - - - -
89B GLU* 3.1 38.4 - - + +
91B SER 3.1 11.4 + - - +
92B ALA* 3.7 8.1 - - - +
94B GLN* 1.3 77.3 - - - +
96B ALA* 1.3 57.2 + - - +
98B TYR* 3.1 7.7 + - - +
99B LYS* 2.8 45.6 + - + +
115B TRP* 3.7 37.0 - - + +
116B HIS 4.4 0.7 - - - -
117B LYS* 3.7 30.5 - - + +
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Residues in contact with ALA 96 (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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92B ALA 3.0 14.9 + - - +
93B GLU* 3.5 11.2 - - - +
94B GLN 3.2 0.2 - - - -
95B ILE* 1.3 76.2 - - - +
97B LYS* 1.3 63.7 + - + +
99B LYS* 3.3 8.9 + - - +
100B GLU* 3.0 32.5 + - + +
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Residues in contact with LYS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B VAL* 5.8 7.3 + - - +
63B ALA* 4.0 20.2 - - + +
93B GLU* 3.1 21.3 + - + +
94B GLN* 3.5 23.7 + - - +
96B ALA* 1.3 73.9 - - + +
98B TYR* 1.3 65.9 + - - +
100B GLU* 3.4 14.9 + - - +
101B LEU* 3.0 24.1 + - - +
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Residues in contact with TYR 98 (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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61B GLY 4.4 1.6 - - - -
62B GLY 3.4 17.3 - - - +
63B ALA 3.1 13.6 + - - +
64B GLY* 3.7 21.1 - - - -
67B ASP* 2.7 38.9 + - - +
68B LEU* 4.3 5.8 - - + -
85B ASN* 3.2 18.6 + - - -
87B VAL* 3.4 24.0 - - + -
89B GLU* 6.0 0.2 - - + -
94B GLN 2.8 12.5 + - - +
95B ILE* 3.3 10.8 - - - +
97B LYS* 1.3 77.9 - - - +
99B LYS* 1.3 61.5 + - - +
101B LEU* 3.1 4.3 + - + +
102B VAL* 3.0 36.3 + - + +
113B PHE* 4.0 8.1 - + - -
115B TRP* 3.1 27.8 - + - +
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Residues in contact with LYS 99 (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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95B ILE* 2.8 34.2 + - + +
96B ALA* 3.6 7.6 - - - +
98B TYR* 1.3 77.6 - - - +
100B GLU* 1.3 62.3 - - + +
102B VAL* 3.3 3.2 + - - +
103B ALA* 3.0 24.3 + - - +
115B TRP* 3.5 48.5 - - + -
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Residues in contact with GLU 100 (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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96B ALA* 3.0 23.0 + - + +
97B LYS* 3.7 13.1 - - - +
98B TYR 3.3 0.2 - - - -
99B LYS* 1.3 75.7 - - + +
101B LEU* 1.3 63.2 + - - +
103B ALA* 3.4 7.6 + - - +
104B LYS* 3.1 33.0 + - + +
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Residues in contact with LEU 101 (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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63B ALA* 3.5 19.3 - - + +
64B GLY* 3.7 5.8 - - - -
65B GLU* 3.7 26.5 - - + +
68B LEU* 3.7 15.7 - - + -
97B LYS 3.0 13.7 + - - +
98B TYR* 3.3 9.2 - - + +
100B GLU* 1.3 76.7 - - - +
102B VAL* 1.3 63.9 + - + +
104B LYS* 3.0 26.1 + - - +
105B ILE* 3.1 41.8 - - + +
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Residues in contact with VAL 102 (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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68B LEU* 4.3 9.6 - - + -
98B TYR* 3.0 40.6 + - + +
99B LYS* 3.6 8.7 - - - +
101B LEU* 1.3 77.3 - - - +
103B ALA* 1.3 61.6 + - - +
105B ILE* 3.2 25.7 + - - +
108B LEU* 4.1 11.0 - - + +
113B PHE* 3.7 40.6 - - + -
115B TRP* 4.0 11.4 - - + -
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Residues in contact with ALA 103 (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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99B LYS 3.0 16.3 + - - +
100B GLU* 3.7 8.5 - - - +
102B VAL* 1.3 79.1 - - - +
104B LYS* 1.3 61.6 + - + +
105B ILE 3.6 3.1 + - - +
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Residues in contact with LYS 104 (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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100B GLU* 3.1 22.5 + - + +
101B LEU* 3.0 21.8 + - - +
103B ALA* 1.3 77.7 - - + +
105B ILE* 1.3 66.6 + - + +
106B SER* 3.4 7.6 + - - -
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Residues in contact with ILE 105 (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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68B LEU* 4.0 17.0 - - + -
101B LEU* 3.1 36.7 + - + +
102B VAL 3.2 15.6 + - - +
103B ALA 4.3 2.8 - - - +
104B LYS* 1.3 83.1 - - + +
106B SER* 1.3 75.5 + - - +
107B ASN 3.9 2.3 + - - +
108B LEU* 3.7 32.8 - - + +
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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