Contacts of the helix formed by residues 102 - 117 (chain A) in PDB entry 1JNK
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 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ASN* 1.3 74.0 - - - +
103A THR* 1.3 58.5 + - - +
105A ALA* 3.8 1.1 - - - +
106A LYS* 2.9 30.3 + - - +
384A GLU* 4.4 16.2 - - - +
385A HIS 3.2 28.6 + - - +
386A THR* 4.7 6.1 - - - +
387A ILE* 4.2 9.7 - - + +
390A TRP* 3.7 19.2 + - + +
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Residues in contact with THR 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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101A ASN* 3.2 8.1 + - - +
102A GLN* 1.3 75.6 - - - +
104A HIS* 1.3 61.9 + - + +
105A ALA 3.1 0.5 + - - -
106A LYS* 3.1 5.0 + - - +
107A ARG* 2.9 33.5 + - + +
217A SER* 3.5 32.3 + - - +
218A PHE 3.9 16.5 + - - -
219A MET* 4.1 20.1 - - + +
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Residues in contact with HIS 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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74A ALA* 3.5 32.5 + - - +
75A GLN* 3.9 20.0 + - + +
97A ARG 5.7 0.2 + - - -
98A PRO* 3.3 18.8 - - + +
100A GLN* 4.6 13.6 + - + -
101A ASN* 2.9 29.2 + - - +
103A THR* 1.3 78.5 - - + +
105A ALA* 1.3 55.9 + - - +
107A ARG* 3.6 11.1 - - + +
108A ALA* 3.0 30.0 + - - +
219A MET* 3.2 34.8 - - + +
221A THR* 5.0 6.5 - - + -
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Residues in contact with ALA 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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98A PRO 3.2 13.6 + - - +
99A PHE* 4.1 5.4 - - - -
101A ASN 2.8 19.0 + - - +
102A GLN 3.9 1.1 - - - +
103A THR 3.1 0.2 - - - -
104A HIS* 1.3 75.8 - - - +
106A LYS* 1.3 65.6 + - - +
109A TYR* 3.0 27.2 + - - +
390A TRP* 3.4 42.7 - - + -
394A ILE* 4.0 8.1 - - + +
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Residues in contact with LYS 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 GLN 2.9 20.8 + - - +
103A THR* 3.6 4.5 - - - +
105A ALA* 1.3 76.0 - - - +
107A ARG* 1.3 64.0 + - - +
109A TYR* 4.0 3.6 - - + +
110A ARG* 3.0 44.0 + - + +
211A ALA* 4.3 19.7 - - + -
381A ASP* 3.0 43.7 + - - +
382A GLU* 3.3 11.9 - - - +
383A ARG* 3.4 20.0 - - - +
390A TRP* 3.7 26.1 - - + -
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLN* 3.5 32.1 + - + +
103A THR* 2.9 19.7 + - + +
104A HIS* 3.6 13.7 - - + +
106A LYS* 1.3 77.4 - - - +
108A ALA* 1.3 63.1 + - - +
110A ARG* 3.3 5.7 + - - +
111A GLU* 3.0 38.8 + - + +
189A ASP* 4.5 7.5 + - - -
191A LYS* 6.1 0.2 - - - +
194A ASN* 5.1 1.0 - - - +
207A ASP* 2.7 39.0 + - - +
208A PHE 4.8 0.4 - - - +
209A GLY* 3.1 27.9 + - - +
210A LEU* 4.4 11.3 - - - +
1001A ANP 6.1 0.4 - - - -
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Residues in contact with ALA 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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75A GLN* 4.6 7.8 - - - +
95A LEU* 4.0 22.1 - - + +
98A PRO* 3.8 23.8 - - + -
104A HIS 3.0 15.4 + - - +
105A ALA 4.0 3.1 - - - +
107A ARG* 1.3 79.0 - - - +
109A TYR* 1.3 64.0 + - - +
111A GLU* 3.5 4.0 + - - +
112A LEU* 3.1 29.3 + - + +
394A ILE* 4.2 8.1 - - + -
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Residues in contact with TYR 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 ALA 3.0 19.4 + - - +
106A LYS* 4.0 6.3 - - - +
108A ALA* 1.3 77.2 - - - +
110A ARG* 1.3 63.5 + - - +
112A LEU* 3.6 5.3 - - - +
113A VAL* 3.0 45.9 + - + +
381A ASP* 4.9 9.4 - - + -
383A ARG* 3.3 31.8 + - - -
390A TRP* 3.9 22.0 - + + -
393A LEU* 3.5 50.7 - - + +
394A ILE* 4.1 15.2 - - + +
397A GLU* 3.8 22.4 + - + -
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Residues in contact with ARG 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 LYS* 3.0 41.3 + - - +
107A ARG* 3.3 5.2 + - - +
109A TYR* 1.3 78.9 - - + +
111A GLU* 1.3 66.9 + - + +
113A VAL* 3.4 2.1 + - - +
114A LEU* 3.1 45.6 + - + +
185A ILE* 4.0 18.0 - - - +
186A ILE 5.1 2.8 + - - +
208A PHE* 3.1 31.0 + - + +
209A GLY 3.8 12.7 + - - -
210A LEU 3.6 31.9 + - - -
211A ALA* 3.9 7.9 - - - +
381A ASP* 4.2 20.6 + - - +
382A GLU* 3.9 14.0 + - - -
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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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75A GLN* 3.3 36.1 + - - +
93A LYS* 4.1 8.9 + - - -
95A LEU* 5.4 0.2 - - - +
107A ARG* 3.0 28.7 + - + +
108A ALA* 3.9 4.9 - - - +
110A ARG* 1.3 76.8 - - + +
112A LEU* 1.3 55.8 + - - +
115A MET* 2.7 57.2 + - + +
144A LEU* 4.6 9.1 - - + +
206A LEU 4.8 0.9 - - - +
207A ASP* 3.5 28.5 - - - +
208A PHE* 4.0 23.7 - - + +
1001A ANP 5.3 0.5 + - - -
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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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95A LEU* 6.2 1.6 - - + -
108A ALA* 3.1 17.6 + - + +
109A TYR* 3.6 7.9 - - - +
110A ARG 3.2 0.2 - - - -
111A GLU* 1.3 81.2 - - - +
113A VAL* 1.3 57.6 + - - +
115A MET* 4.9 4.3 - - - -
116A LYS* 3.2 36.8 + - - +
126A LEU* 4.4 3.7 - - + +
129A VAL* 3.9 24.9 - - + -
142A VAL* 4.9 3.4 - - + -
144A LEU* 3.5 30.7 - - + +
394A ILE* 4.2 12.3 - - + +
397A GLU* 3.7 28.7 - - + -
398A VAL* 3.9 24.0 - - + -
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Residues in contact with VAL 113 (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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109A TYR* 3.0 39.3 + - + +
110A ARG* 3.9 4.5 - - - +
111A GLU 3.3 0.2 - - - -
112A LEU* 1.3 75.9 - - - +
114A LEU* 1.3 62.5 + - + +
116A LYS* 3.6 5.4 + - - +
117A CYS* 3.2 29.2 + - + +
379A GLN 5.5 8.5 - - - +
381A ASP* 4.6 14.6 - - - +
397A GLU* 3.7 31.6 - - - +
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Residues in contact with LEU 114 (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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110A ARG* 3.1 44.4 + - + +
113A VAL* 1.3 79.1 - - + +
115A MET* 1.3 57.2 + - - +
116A LYS 2.9 7.2 + - - -
117A CYS* 3.3 17.9 - - - -
118A VAL* 2.8 33.9 + - + +
185A ILE* 3.7 26.2 - - + -
208A PHE* 3.7 42.4 - - + -
381A ASP* 5.0 9.0 - - - +
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Residues in contact with MET 115 (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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111A GLU* 2.7 52.7 + - + +
112A LEU* 4.6 0.4 - - - +
114A LEU* 1.3 72.2 - - - +
116A LYS* 1.3 58.8 + - - +
118A VAL* 4.0 9.1 - - - +
124A ILE* 3.8 35.8 - - + +
125A SER* 4.7 2.8 - - - -
126A LEU* 3.8 52.6 + - + +
144A LEU* 4.0 23.3 - - + -
146A MET* 4.6 12.8 - - - +
206A LEU 4.9 4.3 - - - +
208A PHE* 3.7 19.9 - - + -
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Residues in contact with LYS 116 (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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112A LEU* 3.2 25.5 - - - +
113A VAL* 3.6 5.1 + - - +
114A LEU 2.9 0.6 - - - -
115A MET* 1.3 79.6 - - - +
117A CYS* 1.3 63.2 + - - +
118A VAL 4.3 2.3 - - - +
119A ASN* 5.9 0.3 - - - +
126A LEU* 3.8 13.5 - - + -
129A VAL* 3.9 25.8 - - - +
397A GLU* 2.8 52.4 + - - +
398A VAL* 4.7 0.4 + - - +
400A ASN* 3.0 18.8 + - - +
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Residues in contact with CYS 117 (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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113A VAL* 3.2 21.9 + - + +
114A LEU* 3.1 29.4 + - - -
116A LYS* 1.3 80.4 - - - +
118A VAL* 1.3 77.4 + - - +
119A ASN* 3.4 8.1 + - - +
373A PRO* 4.9 24.7 - - + +
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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