Contacts of the helix formed by residues 98 - 111 (chain B) in PDB entry 1J30
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 GLN 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B TYR* 3.0 34.2 + - + +
96B TRP 3.5 0.6 - - - -
97B THR* 1.3 98.0 + - - +
99B MET* 1.3 68.2 + - - +
101B PRO* 3.7 4.4 - - - +
102B GLY* 3.1 21.3 + - - -
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Residues in contact with MET 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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15A GLN* 5.0 10.5 - - - +
16A GLY* 4.7 7.4 - - - +
19A GLY* 6.2 4.3 - - - -
94B TYR* 3.0 44.7 + - + +
95B GLU* 3.9 20.9 - - + -
98B GLN* 1.3 80.3 - - - +
100B TYR* 1.3 106.6 + - + +
102B GLY* 3.7 0.5 - - - -
103B PHE* 2.9 63.4 + - + -
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Residues in contact with TYR 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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16A GLY* 4.0 2.0 + - - -
20A GLU* 2.5 33.6 + - - +
60A HIS* 3.0 21.2 + + - -
95B GLU* 3.0 30.8 + - + +
99B MET* 1.3 98.8 - - + +
101B PRO* 1.3 72.8 - - + +
103B PHE* 3.2 12.1 + + - +
104B ALA* 2.9 24.4 + - - +
119B PHE* 3.5 47.0 - + - +
122B LEU* 3.7 24.7 - - + -
123B ALA* 3.7 7.0 - - + -
126B GLU* 3.9 17.9 - - + -
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Residues in contact with PRO 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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95B GLU 3.4 11.7 - - - +
96B TRP 3.1 23.1 - - - +
97B THR 4.3 9.2 - - - +
98B GLN 3.6 11.9 - - - +
100B TYR* 1.3 92.3 - - + +
102B GLY* 1.3 60.7 + - - +
104B ALA* 3.3 7.2 + - + +
105B LYS* 3.1 22.9 + - - +
108B ARG* 4.8 2.1 + - - -
120B GLU* 6.2 0.7 - - + -
123B ALA* 4.2 11.4 - - + -
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Residues in contact with GLY 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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98B GLN 3.1 18.2 + - - -
99B MET 3.7 1.1 - - - -
101B PRO* 1.3 76.4 - - - +
103B PHE* 1.3 65.5 + - - +
105B LYS* 3.4 8.5 + - - +
106B VAL* 3.1 30.1 + - - +
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Residues in contact with PHE 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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9A THR* 4.9 0.2 + - - -
12A ASN* 3.3 64.2 + - + +
15A GLN* 4.4 12.8 - - + -
16A GLY* 4.2 6.3 - - - -
94B TYR* 5.9 0.2 - - - -
99B MET* 2.9 54.6 + - + -
100B TYR* 3.2 22.2 + + - +
102B GLY* 1.3 77.6 - - - +
104B ALA* 1.3 58.3 + - - +
106B VAL* 3.5 2.8 + - + +
107B ALA* 2.9 29.5 + - - +
119B PHE* 3.4 27.0 - + + -
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Residues in contact with ALA 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 TYR 2.9 16.0 + - - +
101B PRO* 3.5 8.3 - - + +
103B PHE* 1.3 76.0 - - - +
105B LYS* 1.3 60.5 + - - +
107B ALA* 3.1 4.1 + - - +
108B ARG* 2.9 38.0 + - - +
116B ALA* 3.6 7.8 - - - +
119B PHE* 3.7 10.7 - - + -
120B GLU* 3.6 35.7 - - + +
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Residues in contact with LYS 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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101B PRO 3.1 12.8 + - - +
102B GLY* 3.6 12.6 - - - +
104B ALA* 1.3 76.1 - - - +
106B VAL* 1.3 60.6 + - + +
108B ARG* 3.4 25.6 + - - +
109B GLU* 3.0 34.7 + - - +
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Residues in contact with VAL 106 (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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8A LYS* 3.9 34.8 - - + -
9A THR* 4.1 1.3 - - - +
12A ASN* 4.1 11.7 - - - +
102B GLY 3.1 16.7 + - - +
103B PHE* 3.8 4.0 - - + +
105B LYS* 1.3 77.6 - - + +
107B ALA* 1.3 64.8 + - - +
109B GLU* 3.0 30.8 - - - +
110B GLU* 2.9 32.2 + - - +
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Residues in contact with ALA 107 (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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9A THR* 3.3 20.6 - - + +
103B PHE 2.9 18.3 + - - +
104B ALA 3.1 5.4 + - - +
106B VAL* 1.3 77.8 - - - +
108B ARG* 1.3 61.1 + - - +
110B GLU 3.4 0.9 + - - -
111B GLY 3.2 5.0 + - - -
112B PHE* 2.8 38.3 + - + +
115B VAL 4.4 1.6 - - - -
116B ALA* 3.7 22.7 - - + +
119B PHE* 4.2 7.9 - - + -
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Residues in contact with ARG 108 (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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101B PRO 4.8 2.0 + - - -
104B ALA* 2.9 16.8 + - - +
105B LYS* 3.5 36.1 - - - +
107B ALA* 1.3 76.3 - - - +
109B GLU* 1.3 62.2 + - - +
111B GLY* 3.2 12.6 + - - -
112B PHE 4.6 3.6 - - - +
113B PRO* 5.0 7.4 - - + +
116B ALA* 3.5 21.8 - - + -
120B GLU* 3.5 24.6 + - - -
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Residues in contact with GLU 109 (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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105B LYS* 3.0 19.9 + - + +
106B VAL* 3.0 45.6 + - - +
108B ARG* 1.3 77.6 - - - +
110B GLU* 1.3 65.8 + - + +
111B GLY 3.2 0.7 + - - -
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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
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7A THR* 3.3 14.2 - - + +
8A LYS* 2.9 26.8 + - - +
9A THR* 2.7 39.5 + - - -
106B VAL* 2.9 25.3 + - + +
108B ARG 3.3 0.2 - - - -
109B GLU* 1.3 86.8 - - + +
111B GLY* 1.3 59.2 + - - +
112B PHE* 3.6 24.0 - - + -
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Residues in contact with GLY 111 (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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107B ALA 3.2 2.0 + - - -
108B ARG 3.2 11.7 + - - -
109B GLU 3.2 1.6 + - - -
110B GLU* 1.3 80.6 - - - +
112B PHE* 1.3 68.0 + - - +
113B PRO* 3.4 13.7 - - - +
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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