Contacts of the helix formed by residues 137 - 158 (chain B) in PDB entry 5JKL
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 TYR 137 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B GLU* 4.1 8.1 - - - -
65B HIS* 2.7 54.4 + + + -
68B LYS* 3.4 20.0 - - + +
69B LEU* 3.4 22.7 + - + +
114B LEU* 3.9 35.0 - - + -
132B PHE* 3.4 36.3 - + - -
133B ILE* 3.0 12.9 + - + +
135B THR 3.8 0.4 - - - -
136B HIS* 1.3 96.7 - - + +
138B LEU* 1.3 66.7 + - - +
139B ASN 3.4 2.0 - - - -
140B GLU* 3.3 6.4 + - + +
141B GLN* 3.0 29.8 + - - +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ASN* 4.2 7.9 - - - +
114B LEU* 3.9 22.2 - - + -
115B LEU* 4.0 27.6 - - + -
118B HIS* 4.3 9.0 - - + -
133B ILE* 3.0 36.6 + - + +
134B GLU* 3.8 31.7 + - + +
137B TYR* 1.3 76.0 - - - +
139B ASN* 1.3 59.1 + - - +
141B GLN* 3.3 6.2 + - - +
142B VAL* 3.0 31.4 + - + +
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Residues in contact with ASN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLU 4.2 8.6 + - - +
135B THR 5.8 2.7 + - - +
136B HIS 5.6 0.2 - - - -
137B TYR 3.4 0.2 - - - -
138B LEU* 1.3 75.7 - - - +
140B GLU* 1.3 61.9 + - - +
142B VAL* 4.0 16.9 - - - +
143B LYS* 2.9 60.9 + - - +
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLU* 5.3 4.2 - - - +
65B HIS* 5.1 19.3 + - + +
135B THR 5.6 2.0 - - - +
136B HIS* 3.3 23.5 - - - +
137B TYR* 3.3 9.3 + - - +
139B ASN* 1.3 78.3 + - - +
141B GLN* 1.3 61.4 + - - +
143B LYS* 3.1 33.2 + - - +
144B ALA* 2.9 29.1 + - - +
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Residues in contact with GLN 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B HIS* 4.6 7.4 - - - -
107B GLU* 2.9 53.2 + - - +
110B VAL* 3.9 11.5 - - - +
111B ASN* 3.4 25.6 - - + +
114B LEU* 3.5 31.7 - - + +
137B TYR* 3.0 13.7 + - - +
138B LEU 3.6 4.3 - - - +
140B GLU* 1.3 77.2 - - - +
142B VAL* 1.3 60.5 + - - +
144B ALA* 3.2 2.6 + - - +
145B ILE* 2.9 36.1 + - + +
201B FE 4.0 13.2 - - - -
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ASN* 5.0 11.4 - - - +
138B LEU* 3.0 21.3 + - + +
139B ASN* 3.8 17.0 - - - +
141B GLN* 1.3 77.4 - - - +
143B LYS* 1.3 65.3 + - + +
145B ILE* 3.9 6.5 - - + +
146B LYS* 3.0 26.3 + - + +
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Residues in contact with LYS 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ASN* 2.9 47.9 + - - +
140B GLU* 3.1 36.1 + - - +
142B VAL* 1.3 74.8 - - + +
144B ALA* 1.3 63.3 + - - +
146B LYS* 3.4 4.8 + - - +
147B GLU* 3.0 24.9 + - - +
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Residues in contact with ALA 144 (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 GLU* 3.9 30.1 - - + +
140B GLU 2.9 19.1 + - - +
141B GLN* 3.2 4.7 + - - +
143B LYS* 1.3 76.7 - - - +
145B ILE* 1.3 57.8 + - - +
147B GLU* 3.4 7.9 + - - +
148B LEU* 3.0 37.4 + - + +
202B MG 4.7 10.5 - - - -
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Residues in contact with ILE 145 (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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104B LEU* 3.8 22.1 - - + +
107B GLU* 3.8 32.8 - - + +
108B LYS* 4.0 27.6 - - + -
111B ASN* 3.8 27.6 - - + +
141B GLN 2.9 22.7 + - - +
142B VAL* 3.9 7.0 - - + +
144B ALA* 1.3 77.2 - - - +
146B LYS* 1.3 60.4 + - - +
148B LEU* 3.5 1.7 + - - -
149B GLY* 2.9 26.5 + - - -
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Residues in contact with LYS 146 (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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142B VAL* 3.0 21.6 + - + +
143B LYS* 3.8 6.1 - - - +
145B ILE* 1.3 78.1 - - - +
147B GLU* 1.3 56.1 + - - +
149B GLY* 3.3 1.8 + - - -
150B ASP* 2.9 69.2 + - - +
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Residues in contact with GLU 147 (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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54B TYR* 2.7 30.3 + - - +
58B GLN* 4.2 6.8 + - - -
143B LYS 3.0 17.7 + - - +
144B ALA* 3.6 8.3 - - - +
145B ILE 3.3 0.2 - - - -
146B LYS* 1.3 76.9 - - - +
148B LEU* 1.3 63.1 + - - +
150B ASP* 3.2 11.4 + - - +
151B HIS* 3.0 46.1 + - + +
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Residues in contact with LEU 148 (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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34B TYR* 3.8 7.9 - - - +
54B TYR* 3.5 25.8 - - + +
58B GLN* 6.4 0.2 - - + -
100B MET* 3.6 26.9 - - - +
103B ALA* 3.7 30.1 - - + +
104B LEU* 3.9 15.9 - - + +
107B GLU* 3.5 33.0 - - + +
144B ALA* 3.0 21.4 + - + +
145B ILE* 4.0 2.7 - - - +
147B GLU* 1.3 73.8 - - - +
149B GLY* 1.3 65.9 + - - +
151B HIS* 3.2 4.3 + - + +
152B VAL* 2.9 31.4 + - - +
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Residues in contact with GLY 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 4.4 15.4 - - - +
145B ILE 2.9 17.4 + - - -
146B LYS* 3.7 2.2 - - - -
147B GLU 3.3 0.2 - - - -
148B LEU* 1.3 78.1 - - - +
150B ASP* 1.3 61.4 + - - +
152B VAL* 3.3 3.4 + - - +
153B THR* 3.0 28.8 + - - -
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Residues in contact with ASP 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LYS* 2.9 55.3 + - - +
147B GLU* 3.4 11.4 - - - +
149B GLY* 1.3 74.5 - - - +
151B HIS* 1.3 68.4 + - + +
153B THR* 3.4 6.1 + - - -
154B ASN* 3.0 37.2 + - - +
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Residues in contact with HIS 151 (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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54B TYR* 3.8 20.8 + + - -
100B MET* 3.9 32.1 - - + -
147B GLU* 3.0 39.8 + - + +
148B LEU* 3.2 6.5 + - - +
150B ASP* 1.3 78.8 - - + +
152B VAL* 1.3 65.3 + - - +
154B ASN* 3.3 3.2 + - - +
155B LEU* 3.0 30.4 + - - +
170B PHE* 3.5 23.1 - + + -
174B THR* 3.8 23.5 - - + +
175B LEU* 4.0 10.9 - - + +
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Residues in contact with VAL 152 (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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97B LEU* 3.9 12.5 - - + +
100B MET* 3.8 35.2 - - + +
101B GLU* 3.9 10.8 - - + +
104B LEU* 4.6 12.1 - - + -
148B LEU 2.9 20.9 + - - +
149B GLY* 3.6 6.5 - - - +
151B HIS* 1.3 77.0 - - - +
153B THR* 1.3 57.2 + - - +
155B LEU* 3.4 1.8 + - - +
156B ARG* 2.9 72.5 + - - +
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Residues in contact with THR 153 (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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149B GLY 3.0 18.0 + - - -
150B ASP* 3.6 8.5 - - - +
152B VAL* 1.3 77.4 - - - +
154B ASN* 1.3 61.5 + - - +
156B ARG* 3.3 11.8 + - - +
157B LYS* 2.9 57.1 + - + +
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Residues in contact with ASN 154 (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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150B ASP* 3.0 33.7 + - - +
151B HIS* 3.9 1.4 + - - +
153B THR* 1.3 79.5 - - - +
155B LEU* 1.3 58.3 + - - +
157B LYS* 3.7 6.1 - - - +
158B MET* 2.8 43.6 + - - +
170B PHE* 3.8 23.6 - - + -
174B THR* 5.7 2.0 - - - -
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Residues in contact with LEU 155 (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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51B PHE* 4.2 6.7 - - + -
97B LEU* 4.0 32.3 - - + +
100B MET* 4.0 20.9 - - + -
151B HIS 3.0 21.7 + - - +
152B VAL 3.8 2.9 - - - +
154B ASN* 1.3 76.8 - - - +
156B ARG* 1.3 63.1 + - - +
158B MET* 3.4 9.1 + - - +
159B GLY 3.4 0.2 + - - -
160B ALA* 3.0 32.4 + - + +
166B ALA 4.4 2.5 - - - +
167B GLU* 4.2 27.1 - - + -
170B PHE* 3.7 44.2 - - + -
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Residues in contact with ARG 156 (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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97B LEU* 4.0 16.2 - - + -
101B GLU* 2.8 30.5 + - - +
104B LEU* 6.3 0.4 - - - +
152B VAL* 2.9 40.9 + - - +
153B THR* 3.7 10.5 + - - +
155B LEU* 1.3 77.0 - - - +
157B LYS* 1.3 62.9 + - + +
159B GLY* 3.2 15.1 + - - -
160B ALA 4.3 8.9 + - - +
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Residues in contact with LYS 157 (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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153B THR* 2.9 43.2 + - + +
154B ASN* 3.7 7.4 - - - +
156B ARG* 1.3 73.1 - - + +
158B MET* 1.3 61.6 + - + +
159B GLY* 3.2 1.4 + - - -
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Residues in contact with MET 158 (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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154B ASN* 2.8 36.5 + - + +
155B LEU* 3.7 4.9 - - - +
156B ARG 3.3 0.4 - - - -
157B LYS* 1.3 77.6 - - + +
159B GLY* 1.3 55.4 + - - +
160B ALA 3.7 0.2 - - - -
163B SER* 4.4 4.3 + - - -
166B ALA* 3.3 44.8 - - + +
169B LEU* 4.0 15.0 - - + -
170B PHE* 3.8 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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