Contacts of the helix formed by residues 138 - 156 (chain B) in PDB entry 3EJW
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 VAL 138 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LYS* 3.5 27.4 - - + +
66B SER 3.6 17.0 - - - +
67B VAL* 3.3 18.8 + - + +
134B SER* 3.4 23.6 - - - +
135B SER* 3.1 23.3 + - - +
137B THR* 1.3 77.4 + - - +
139B THR* 1.3 70.3 + - - +
140B ASP* 3.6 4.0 - - - +
141B GLN* 3.9 19.1 - - + +
142B ASN* 2.8 29.0 + - - +
169B ASN* 6.3 0.4 - - - +
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Residues in contact with THR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL 4.4 0.6 + - - -
68B SER* 3.4 3.1 + - - -
69B PRO* 3.1 35.5 - - + +
91B SER* 3.5 6.0 + - - -
92B ASP* 2.8 41.8 + - + +
93B VAL* 5.2 1.1 - - - -
94B ASN* 5.9 0.9 - - - +
137B THR 3.5 2.6 + - - -
138B VAL* 1.3 80.3 - - - +
140B ASP* 1.3 66.4 + - - +
142B ASN* 4.2 1.3 - - - +
143B ALA* 3.3 20.2 + - + +
285B GLN* 6.3 0.7 - - - +
287B TYR* 4.4 9.0 - - + +
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Residues in contact with ASP 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LYS* 2.9 25.5 + - - -
90B ASP* 3.3 23.1 - - - +
91B SER* 3.2 17.9 + - - +
92B ASP 5.4 0.4 - - - +
101B TYR* 4.6 3.8 - - - +
138B VAL* 3.6 4.0 - - - +
139B THR* 1.3 77.7 - - - +
141B GLN* 1.3 81.1 + - - +
143B ALA* 3.1 5.9 + - - +
144B TRP* 3.0 49.3 + - + +
285B GLN* 6.0 2.2 - - - +
400B PAV 2.7 24.0 + - - -
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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
----------------------------------------------------------
9B LYS* 3.6 10.9 - - - +
133B TYR* 3.2 20.3 - - + +
134B SER* 2.6 41.9 + - - -
138B VAL* 3.9 6.7 + - + -
139B THR 3.6 0.4 - - - -
140B ASP* 1.3 84.4 + - - +
142B ASN* 1.3 56.1 + - - +
144B TRP* 3.8 11.3 - - + +
145B ALA* 2.9 31.0 + - - +
169B ASN* 4.8 0.2 + - - -
194B PRO* 3.0 26.1 + - + +
195B ASP* 2.9 22.9 + - - -
400B PAV 3.0 30.9 + - - +
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Residues in contact with ASN 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B TYR* 2.9 26.2 + - - -
135B SER 2.9 25.1 + - - -
136B PRO* 3.2 28.8 - - - +
137B THR 3.7 0.8 - - - -
138B VAL* 2.8 28.5 + - - +
139B THR* 4.2 1.6 - - - +
140B ASP 3.2 0.4 - - - -
141B GLN* 1.3 76.9 - - - +
143B ALA* 1.3 63.5 - - - +
145B ALA 4.4 0.2 - - - +
146B GLU* 3.0 38.9 + - + +
166B TYR* 4.5 1.2 + - - -
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PRO* 3.9 25.3 - - + +
139B THR* 3.3 13.1 + - + +
140B ASP* 3.1 11.1 + - - +
142B ASN* 1.3 78.0 - - - +
144B TRP* 1.3 66.1 + - + +
146B GLU* 4.1 3.3 - - - +
147B ALA* 3.1 22.3 + - - +
285B GLN* 5.0 6.3 - - - +
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Residues in contact with TRP 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ASP 4.6 0.7 - - - -
101B TYR* 5.4 1.3 + - - -
103B ASN* 5.5 1.0 + - - -
104B GLN* 3.2 32.5 - - - -
105B GLY 4.5 4.9 + - - -
107B PRO* 4.0 15.4 - - + +
110B LEU* 3.4 32.9 - - + +
111B GLY* 3.5 12.7 - - - +
114B LEU* 4.4 10.5 - - + -
140B ASP* 3.0 36.8 + - + +
141B GLN* 3.8 18.6 - - + +
143B ALA* 1.3 80.4 - - + +
145B ALA* 1.3 57.7 + - - +
147B ALA* 3.2 6.9 + - - +
148B ALA* 2.8 30.4 + - - +
194B PRO* 4.1 6.3 - - + -
220B PHE* 3.5 32.3 - + - -
241B TRP* 3.9 5.4 - + - -
285B GLN* 5.2 5.3 - - - +
400B PAV 3.5 24.2 - - - -
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 5.2 2.7 - - - +
131B PHE* 4.1 18.1 - - + -
133B TYR* 3.6 35.0 - - + +
141B GLN 2.9 18.8 + - - +
142B ASN 4.0 2.2 - - - +
143B ALA 3.4 0.2 - - - -
144B TRP* 1.3 76.5 - - - +
146B GLU* 1.3 60.4 + - - +
148B ALA* 3.3 1.8 + - - +
149B LYS* 2.8 38.8 + - - +
194B PRO* 5.0 2.7 - - + -
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Residues in contact with GLU 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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228A PRO* 6.0 1.7 - - - +
133B TYR* 4.8 7.4 + - - -
142B ASN* 3.0 25.2 + - + +
143B ALA* 4.2 4.0 - - - +
145B ALA* 1.3 74.3 - - - +
147B ALA* 1.3 65.8 + - - +
149B LYS* 3.8 26.4 + - - +
150B ALA* 3.0 24.9 + - - +
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Residues in contact with ALA 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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107B PRO* 3.2 35.4 - - + +
108B GLU* 4.2 11.0 - - + +
111B GLY* 4.2 3.3 - - - -
143B ALA 3.1 18.6 + - - +
144B TRP 3.4 3.1 - - - +
146B GLU* 1.3 78.7 - - - +
148B ALA* 1.3 61.0 + - - +
150B ALA* 3.4 6.0 + - - +
151B LYS* 3.1 22.7 + - - +
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Residues in contact with ALA 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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111B GLY* 3.5 21.9 - - - +
114B LEU* 4.6 7.0 - - + -
115B VAL* 3.5 16.5 - - + +
131B PHE* 3.9 19.3 - - + -
144B TRP 2.8 17.4 + - - +
145B ALA* 3.3 4.9 + - - +
147B ALA* 1.3 75.2 - - - +
149B LYS* 1.3 60.7 + - - +
151B LYS* 3.3 1.2 + - - -
152B ILE* 2.9 35.2 + - - +
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Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PHE* 3.9 35.4 - - + -
133B TYR* 4.9 2.4 + - - -
145B ALA* 2.8 22.5 + - - +
146B GLU* 3.8 29.4 + - - +
147B ALA 3.3 0.2 - - - -
148B ALA* 1.3 77.3 - - - +
150B ALA* 1.3 55.9 + - - +
152B ILE* 3.2 6.5 + - - +
153B ALA* 2.9 31.7 + - - +
161B ILE* 4.5 14.7 - - + +
164B THR* 2.8 37.1 + - - +
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Residues in contact with ALA 150 (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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146B GLU 3.0 16.4 + - - +
147B ALA* 3.8 6.7 - - - +
149B LYS* 1.3 77.2 - - - +
151B LYS* 1.3 61.8 + - - +
153B ALA* 3.6 5.9 + - - +
154B LYS* 3.1 24.3 + - - +
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Residues in contact with LYS 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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112B GLY* 3.6 28.5 - - - +
115B VAL* 3.7 24.7 - - + -
116B ASP* 3.5 26.9 + - - -
147B ALA 3.1 16.6 + - - +
148B ALA* 3.6 6.3 - - - +
149B LYS 3.3 0.2 - - - -
150B ALA* 1.3 78.0 - - - +
152B ILE* 1.3 55.6 + - - +
154B LYS* 3.3 6.1 + - - +
155B GLU* 2.6 71.6 + - + +
156B HIS* 5.5 0.7 - - - -
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Residues in contact with ILE 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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115B VAL* 3.8 20.2 - - + -
129B VAL* 5.1 0.2 - - + -
131B PHE* 3.9 30.3 - - + -
148B ALA 2.9 20.3 + - - +
149B LYS* 3.6 5.8 - - - +
151B LYS* 1.3 72.8 - - - +
153B ALA* 1.3 64.1 + - - +
154B LYS 3.0 1.3 - - - -
156B HIS* 2.8 41.4 + - + +
159B TRP* 3.8 55.2 - - + +
161B ILE* 4.1 16.2 - - + -
192B ILE* 4.1 6.1 - - + -
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Residues in contact with ALA 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 LYS 2.9 16.3 + - - +
150B ALA* 3.9 6.7 - - - +
152B ILE* 1.3 78.5 - - - +
154B LYS* 1.3 61.8 + - - +
156B HIS 5.0 0.9 - - - -
157B PRO* 4.0 16.9 - - - +
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Residues in contact with LYS 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 ALA 3.1 17.5 + - - +
151B LYS* 3.7 4.5 - - - +
152B ILE 3.0 0.6 - - - -
153B ALA* 1.3 80.9 - - - +
155B GLU* 1.3 91.4 + - + +
157B PRO* 3.9 10.2 - - - +
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Residues in contact with GLU 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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125B GLU* 5.7 0.5 - - - +
151B LYS* 2.6 58.6 + - - +
154B LYS* 1.3 107.3 + - + +
156B HIS* 1.3 76.2 + - + +
157B PRO* 3.4 11.1 - - - +
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Residues in contact with HIS 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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115B VAL* 3.5 33.3 - - + +
116B ASP* 5.7 1.2 + - - -
119B ALA* 4.0 17.8 - - + +
125B GLU* 5.3 3.4 + - - -
151B LYS* 5.5 0.6 - - - -
152B ILE* 2.8 21.3 + - + +
155B GLU* 1.3 97.9 + - + +
157B PRO* 1.3 60.1 - - - +
158B GLY 3.1 2.7 - - - -
159B TRP* 2.9 70.6 + + + +
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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
------------------------------------------------------------
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