Contacts of the helix formed by residues 99 - 114 (chain A) in PDB entry 1JK7
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLY* 3.6 13.5 - - - -
26A LYS 3.0 26.5 + - - -
27A ASN* 3.1 21.8 + - - +
67A GLY 2.9 15.1 + - - +
69A TYR* 3.7 13.4 + - + +
70A TYR* 3.2 29.7 - - - -
98A LYS* 1.3 91.6 - - + +
100A SER* 1.3 59.3 + - - +
101A LEU 3.2 1.8 - - - -
102A GLU* 3.3 27.4 + - - +
103A THR* 2.7 29.8 + - - -
139A GLU* 3.6 4.5 - - - -
143A ARG* 4.7 0.7 - - - +
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Residues in contact with SER 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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67A GLY* 3.6 14.5 - - - -
93A TYR 4.5 0.7 - - - -
94A VAL* 3.4 11.5 - - - +
95A ASP* 2.9 28.2 + - - -
97A GLY 4.4 2.9 + - - -
99A GLN* 1.3 73.4 - - - +
101A LEU* 1.3 58.2 + - - +
103A THR* 3.2 1.7 + - - -
104A ILE* 2.8 35.2 + - - +
135A GLY 5.4 0.3 - - - -
136A PHE* 3.5 26.0 - - - -
139A GLU* 2.9 17.7 + - - -
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Residues in contact with LEU 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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35A ILE* 4.9 4.0 - - + -
100A SER* 1.3 77.2 - - - +
102A GLU* 1.3 67.9 + - - +
104A ILE* 3.4 2.8 - - - +
105A CYS* 3.0 32.6 + - - -
136A PHE* 3.8 13.0 - - + -
139A GLU* 2.8 33.3 + - + +
140A CYS* 4.0 8.1 - - - -
143A ARG* 3.7 24.9 - - + +
144A TYR* 3.7 36.8 - - + -
148A LEU* 5.3 0.2 - - + -
152A PHE* 3.8 32.1 - - + -
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Residues in contact with GLU 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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16A LEU* 4.2 10.8 - - + +
27A ASN* 3.3 7.4 - - - -
28A VAL* 2.8 47.7 + - + +
69A TYR* 3.4 44.9 - - + -
99A GLN* 3.3 21.6 + - - +
101A LEU* 1.3 73.5 - - - +
103A THR* 1.3 64.1 + - - +
105A CYS* 4.0 0.7 - - - +
106A LEU* 3.0 20.1 + - - +
143A ARG* 2.8 36.4 + - - -
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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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65A ILE* 3.7 24.7 - - + -
67A GLY* 3.4 14.4 - - - +
69A TYR* 3.4 20.1 + - - -
72A LEU* 3.9 11.1 - - + +
93A TYR 3.5 20.9 - - - +
99A GLN 2.7 20.6 + - - -
100A SER 3.4 4.5 - - - -
101A LEU 3.2 0.2 - - - -
102A GLU* 1.3 80.8 - - - +
104A ILE* 1.3 64.3 + - - +
106A LEU* 3.4 2.1 + - - +
107A LEU* 3.2 35.6 + - + +
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Residues in contact with ILE 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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93A TYR* 4.0 27.8 + - + -
94A VAL* 4.2 9.2 - - + -
100A SER 2.8 25.6 + - - +
101A LEU* 3.4 8.3 - - - +
103A THR* 1.3 74.8 - - - +
105A CYS* 1.3 59.7 + - - +
107A LEU* 3.4 7.6 + - + -
108A LEU* 2.8 59.4 + - + +
120A LEU* 5.2 0.9 - - + -
136A PHE* 4.3 7.4 - - + -
152A PHE* 3.6 25.8 - - + -
156A PHE* 3.9 31.9 - - + -
159A LEU* 6.3 0.4 - - + -
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Residues in contact with CYS 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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16A LEU* 3.9 7.6 - - + -
30A LEU* 4.0 15.5 - - + -
35A ILE* 3.9 41.1 - - - -
38A LEU* 3.8 23.6 - - + +
101A LEU* 3.0 27.8 + - - +
102A GLU* 4.0 2.7 - - - +
104A ILE* 1.3 73.5 - - - +
106A LEU* 1.3 61.2 + - - +
108A LEU* 4.6 2.9 - - - -
109A ALA* 2.8 31.9 + - - +
152A PHE* 4.4 9.4 - - - -
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Residues in contact with LEU 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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13A ILE* 4.7 9.2 - - + -
16A LEU* 3.6 23.7 - - + +
17A LEU* 4.0 17.5 - - + -
69A TYR* 3.7 27.4 - - + +
72A LEU* 4.2 4.3 - - + -
73A LEU* 4.0 13.7 - - + -
76A PHE* 3.9 23.8 - - + -
102A GLU 3.0 18.2 + - - +
103A THR 3.9 2.7 - - - +
105A CYS* 1.3 75.9 - - - +
107A LEU* 1.3 63.5 + - - +
109A ALA* 3.3 1.1 + - - +
110A TYR* 3.0 48.9 + - + -
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Residues in contact with LEU 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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65A ILE* 5.0 1.3 - - + -
72A LEU* 4.0 16.4 - - + -
76A PHE* 4.3 3.6 - - + -
89A PHE* 3.8 26.5 - - + -
93A TYR* 3.3 46.7 - - + -
103A THR* 3.2 26.5 + - + +
104A ILE* 3.7 5.4 - - + +
106A LEU* 1.3 77.0 - - - +
108A LEU* 1.3 63.0 + - - +
110A TYR 3.3 0.9 + - - -
111A LYS* 3.0 19.8 + - - +
118A PHE* 3.2 33.1 - - + -
120A LEU* 4.0 16.1 - - + +
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Residues in contact with LEU 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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38A LEU* 4.3 25.4 - - + +
39A CYS* 4.3 2.7 - - - -
42A SER* 3.7 25.4 - - - +
46A PHE* 4.0 22.4 - - + -
104A ILE* 2.8 53.5 + - + +
105A CYS* 3.9 4.0 - - - +
107A LEU* 1.3 74.1 - - - +
109A ALA* 1.3 63.2 + - - +
111A LYS* 3.2 5.6 + - - +
112A ILE* 3.0 30.3 + - - +
120A LEU* 4.1 6.1 - - + -
152A PHE* 4.2 16.2 - - + -
155A CYS* 4.3 11.4 - - - -
156A PHE* 5.5 1.3 - - + -
159A LEU* 5.6 1.1 - - + -
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Residues in contact with ALA 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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9A ILE* 3.9 6.7 - - + +
12A ILE* 4.5 9.6 - - + -
13A ILE* 3.8 24.0 - - + -
16A LEU* 4.6 0.7 - - + -
38A LEU* 3.9 19.9 - - + +
105A CYS 2.8 19.2 + - - +
106A LEU* 3.5 8.7 - - - +
108A LEU* 1.3 77.3 - - - +
110A TYR* 1.3 58.4 + - - +
112A ILE* 3.3 4.8 + - - +
113A LYS* 2.9 29.6 + - - +
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Residues in contact with TYR 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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13A ILE* 4.0 24.9 - - + -
17A LEU* 3.4 25.8 - - + +
76A PHE* 3.9 19.7 - + - -
81A PHE* 3.6 16.3 - - - +
82A PRO* 3.7 45.5 + - + +
106A LEU* 3.0 44.5 + - + +
108A LEU 3.3 0.2 - - - -
109A ALA* 1.3 73.6 - - - +
111A LYS* 1.3 57.9 + - - +
113A LYS* 4.1 1.3 - - - -
114A TYR* 2.7 53.1 + + + +
118A PHE* 3.7 26.7 - + + +
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Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A SER* 4.9 4.7 - - - -
45A ILE* 3.7 21.3 - - + +
46A PHE* 3.6 34.5 - - + -
49A GLN* 2.9 22.8 + - - -
107A LEU 3.0 13.8 + - - +
108A LEU* 3.2 13.0 + - - +
110A TYR* 1.3 75.8 - - - +
112A ILE* 1.3 58.6 + - + +
115A PRO* 2.8 54.8 + - - +
118A PHE* 2.7 38.6 + - + +
119A PHE* 3.3 16.2 - - - +
120A LEU* 4.5 6.5 - - + +
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Residues in contact with ILE 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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9A ILE* 4.0 23.6 - - + -
38A LEU* 3.5 46.0 - - + +
41A LYS* 3.7 36.7 + - + +
42A SER* 4.0 18.4 - - - +
45A ILE* 3.6 12.6 - - + +
108A LEU 3.0 14.2 + - - +
109A ALA 3.6 5.2 - - - +
111A LYS* 1.3 77.4 - - - +
113A LYS* 1.3 60.4 + - - +
115A PRO* 3.4 11.4 - - - +
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Residues in contact with LYS 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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9A ILE* 4.0 18.4 - - + +
10A ASP* 2.8 33.9 + - - +
13A ILE* 4.1 11.9 - - + -
109A ALA 2.9 17.3 + - - +
110A TYR* 3.8 3.6 - - - +
112A ILE* 1.3 79.6 - - - +
114A TYR* 1.3 104.7 + - + +
115A PRO* 3.4 4.7 - - - +
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Residues in contact with TYR 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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82A PRO* 3.8 22.4 + - + -
83A PRO* 3.1 48.1 - - + +
110A TYR* 2.7 33.2 + + + +
111A LYS 3.5 3.1 - - - -
113A LYS* 1.3 118.6 - - + +
115A PRO* 1.3 60.8 - - - +
116A GLU 3.2 2.9 - - - -
117A ASN* 3.0 22.4 + - + +
118A PHE* 3.0 31.8 + - + +
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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