Contacts of the helix formed by residues 98 - 112 (chain A) in PDB entry 1JSX
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 LEU 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ASP* 3.0 11.6 + - - +
97A SER* 1.3 83.9 - - - +
99A GLY* 1.3 68.8 + - - +
100A LYS* 4.3 7.2 - - + +
101A ARG* 2.9 55.7 + - - +
102A VAL* 3.3 9.6 + - - +
121A GLN* 4.1 2.2 - - - -
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Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 1.3 73.2 - - - +
100A LYS* 1.3 54.8 + - - +
102A VAL* 3.6 4.6 - - - +
103A ARG* 2.9 48.7 + - - +
121A GLN* 3.1 35.2 - - - +
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TRP* 3.8 26.2 - - + -
98A LEU* 2.9 7.5 + - + +
99A GLY* 1.3 77.9 - - - +
101A ARG* 1.3 68.1 + - - +
103A ARG* 3.6 27.6 + - - +
104A PHE* 3.3 15.2 + - - +
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Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TRP* 3.8 30.6 - - + -
75A GLY* 3.5 35.6 - - - +
76A PRO* 5.8 1.1 - - - -
96A ASP* 2.8 37.8 + - + +
98A LEU* 2.9 43.0 + - - +
100A LYS* 1.3 77.9 - - - +
102A VAL* 1.3 62.8 + - - +
104A PHE* 3.0 5.5 + - - +
105A LEU* 2.9 32.9 + - + +
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ASP* 4.0 10.8 - - + +
98A LEU 3.9 7.6 - - - +
99A GLY* 3.3 9.8 + - - +
101A ARG* 1.3 77.8 - - - +
103A ARG* 1.3 61.5 + - - +
105A LEU* 3.3 12.9 + - + +
106A ARG* 3.0 54.2 + - - +
119A PRO* 4.1 11.2 - - + -
120A VAL 3.5 21.5 - - - +
121A GLN* 3.5 32.8 - - + +
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Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A GLY* 2.9 41.4 + - - +
100A LYS* 3.6 28.5 - - - +
102A VAL* 1.3 72.3 - - + +
104A PHE* 1.3 66.0 + - - +
106A ARG* 3.2 23.0 + - - +
107A GLN* 3.2 27.8 + - - +
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Residues in contact with PHE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A TYR* 4.3 4.5 - + - -
30A MET* 3.6 44.2 - - + -
31A LEU* 3.9 5.2 - - + -
34A TRP* 3.6 42.4 - + + -
76A PRO* 3.4 46.7 - - + -
100A LYS 3.3 3.8 + - - +
101A ARG* 3.0 8.6 + - - +
103A ARG* 1.3 77.2 - - - +
105A LEU* 1.3 60.0 + - + +
107A GLN* 2.8 39.3 + - - +
108A VAL* 2.9 32.6 + - + +
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A THR* 3.4 28.5 - - + -
75A GLY 3.7 4.5 - - - +
76A PRO* 3.5 34.8 - - + +
77A GLY* 3.5 9.9 - - - +
81A ILE* 4.3 11.4 - - + -
94A LEU* 4.0 22.9 - - + +
96A ASP* 5.3 0.2 - - + -
101A ARG* 2.9 18.6 + - + +
102A VAL* 3.5 17.0 - - + +
104A PHE* 1.3 76.9 - - + +
106A ARG* 1.3 57.2 + - - +
108A VAL* 3.4 7.4 + - + +
109A GLN* 2.9 28.4 + - - +
117A ILE* 4.3 2.9 - - - +
119A PRO* 3.8 16.6 - - + +
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Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A VAL* 3.0 38.6 + - - +
103A ARG* 3.5 23.1 - - - +
105A LEU* 1.3 73.2 - - - +
107A GLN* 1.3 66.0 + - - +
109A GLN* 3.4 17.3 + - - +
110A HIS* 3.0 20.8 + - - +
119A PRO* 4.1 24.3 + - + +
120A VAL* 5.4 2.0 - - - +
121A GLN* 5.6 1.4 - - - +
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Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A MET* 3.8 21.1 - - + +
103A ARG* 3.2 16.6 + - - +
104A PHE* 2.8 24.5 + - - +
106A ARG* 1.3 73.0 - - + +
108A VAL* 1.3 57.5 + - - +
110A HIS* 2.9 9.7 + - - +
111A GLU* 2.7 37.5 + - + +
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Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A TYR* 4.0 18.4 - - + -
30A MET* 3.9 19.1 - - + -
81A ILE* 4.1 18.2 - - + -
104A PHE* 2.9 47.7 + - + +
105A LEU* 3.5 11.4 - - + +
107A GLN* 1.3 76.6 - - - +
109A GLN* 1.3 57.6 + - - +
110A HIS 3.1 0.3 + - - -
111A GLU 3.1 0.2 + - - -
112A LEU* 2.8 57.0 + - + +
114A LEU* 4.3 1.8 - - + -
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Residues in contact with GLN 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU 2.9 17.7 + - - +
106A ARG* 3.4 15.1 - - - +
107A GLN 3.2 0.2 - - - -
108A VAL* 1.3 75.7 - - - +
110A HIS* 1.3 57.7 + - - +
113A LYS* 3.0 22.0 + - - -
114A LEU* 3.1 31.4 + - - +
115A GLU* 5.7 1.0 - - - +
117A ILE* 3.0 49.3 + - + +
119A PRO* 3.6 18.7 - - - +
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Residues in contact with HIS 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ARG 3.0 12.5 + - - +
107A GLN* 2.9 12.4 + - - +
109A GLN* 1.3 76.7 - - - +
111A GLU* 1.3 77.6 + - + +
113A LYS* 3.3 19.3 + - - +
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA* 5.3 2.7 - - + -
30A MET* 3.7 36.3 - - + -
107A GLN* 2.7 19.0 + - + +
108A VAL 3.8 0.2 - - - +
110A HIS* 1.3 89.0 - - + +
112A LEU* 1.3 66.0 + - + +
113A LYS* 3.2 6.8 + - - +
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A HIS* 5.0 3.8 - - - -
23A GLN* 2.9 58.1 + - + +
26A ALA* 3.2 35.0 - - + -
27A TYR* 3.8 12.6 - - + +
30A MET* 4.6 1.6 - - - -
81A ILE* 4.3 0.7 - - + -
85A ILE* 3.9 17.3 - - + -
108A VAL* 2.8 40.9 + - + +
111A GLU* 1.3 78.2 - - + +
113A LYS* 1.3 66.4 + - - +
114A LEU* 3.9 18.2 - - + -
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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