Contacts of the helix formed by residues 138 - 156 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LYS* 3.4 34.5 - - + +
66A SER 3.6 12.6 - - - +
67A VAL* 3.5 16.8 - - + +
134A SER* 3.6 21.3 - - - +
135A SER* 3.1 16.3 + - - +
137A THR* 1.3 77.8 + - - +
139A THR* 1.3 68.9 + - - +
140A ASP* 3.5 12.1 - - - +
141A GLN* 3.8 13.2 - - + +
142A ASN* 2.8 34.2 + - - +
169A ASN* 6.3 0.7 - - - +
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Residues in contact with THR 139 (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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66A SER 4.6 0.2 + - - -
67A VAL 4.7 0.2 + - - -
68A SER* 3.4 3.5 + - - -
69A PRO* 3.2 35.7 - - + -
91A SER* 3.4 6.1 + - - -
92A ASP* 2.8 42.4 + - + +
93A VAL* 5.2 1.8 - - - -
94A ASN* 6.1 0.2 - - - +
137A THR 3.4 3.0 + - - -
138A VAL* 1.3 77.8 - - - +
140A ASP* 1.3 66.5 + - - +
142A ASN* 4.3 1.1 - - - +
143A ALA* 3.2 24.0 + - + +
287A TYR* 4.6 9.9 - - + +
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Residues in contact with ASP 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS* 2.8 26.6 + - - -
90A ASP* 3.4 22.1 - - - +
91A SER* 3.2 13.1 + - - +
92A ASP 5.4 0.2 - - - +
101A TYR* 4.5 3.4 - - - +
138A VAL* 3.5 3.6 - - - +
139A THR* 1.3 77.5 - - - +
141A GLN* 1.3 81.2 + - - +
143A ALA* 3.2 5.6 + - - +
144A TRP* 3.0 51.7 + - + +
285A GLN* 6.1 1.6 - - - +
400A PAV 2.6 28.3 + - - -
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Residues in contact with GLN 141 (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 LYS* 3.7 4.6 - - - +
133A TYR* 3.2 17.7 - - + +
134A SER* 2.6 40.3 + - - -
138A VAL* 3.8 7.3 - - + +
139A THR 3.5 0.4 - - - -
140A ASP* 1.3 89.4 + - - +
142A ASN* 1.3 58.4 + - - +
144A TRP* 3.3 11.4 + - + +
145A ALA* 2.8 31.2 + - - +
169A ASN* 4.9 0.4 + - - -
194A PRO* 3.1 27.6 + - + +
195A ASP* 2.8 23.6 + - - -
400A PAV 3.0 29.0 + - - +
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Residues in contact with ASN 142 (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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133A TYR* 2.8 29.4 + - - -
135A SER 2.9 24.0 + - - -
136A PRO* 3.2 28.5 + - - +
137A THR 3.7 0.8 - - - +
138A VAL* 2.8 27.0 + - - +
139A THR 4.3 0.9 - - - +
140A ASP 3.3 0.6 - - - -
141A GLN* 1.3 72.4 - - - +
143A ALA* 1.3 66.5 + - - +
145A ALA* 3.9 0.3 - - - +
146A GLU* 2.9 26.5 + - - +
166A TYR* 4.5 1.0 + - - -
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Residues in contact with ALA 143 (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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107A PRO* 4.0 22.8 - - + +
139A THR* 3.2 15.6 + - + +
140A ASP* 3.2 11.6 + - - +
142A ASN* 1.3 77.3 - - - +
144A TRP* 1.3 65.0 + - + +
146A GLU* 3.4 5.3 + - - +
147A ALA* 3.1 22.5 + - - +
285A GLN* 5.0 6.3 - - - +
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Residues in contact with TRP 144 (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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90A ASP 4.5 0.9 - - - -
101A TYR* 5.2 2.5 + - - -
103A ASN* 5.4 0.4 + - - -
104A GLN* 3.3 29.8 - - - -
105A GLY 4.7 4.0 + - - -
107A PRO* 4.0 23.3 - - + +
110A LEU* 3.3 31.6 - - + +
111A GLY* 3.6 10.1 - - - +
114A LEU* 4.4 13.5 - - + -
140A ASP* 3.0 43.9 + - + +
141A GLN* 3.7 17.5 - - + +
143A ALA* 1.3 77.7 - - + +
145A ALA* 1.3 61.8 + - - +
147A ALA 3.3 0.7 + - - -
148A ALA* 2.8 29.9 + - - +
194A PRO* 4.1 7.4 - - + -
220A PHE* 3.6 30.7 - + - -
241A TRP* 4.0 5.4 - + - -
285A GLN* 5.0 6.1 - - - +
400A PAV 3.5 21.8 - - - -
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Residues in contact with ALA 145 (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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114A LEU* 5.2 0.4 - - - +
131A PHE* 4.1 21.1 - - + -
133A TYR* 3.6 35.7 - - + +
141A GLN 2.8 20.9 + - - +
142A ASN 3.9 2.0 - - - +
144A TRP* 1.3 70.3 - - - +
146A GLU* 1.3 61.3 + - - +
148A ALA* 3.2 1.3 + - - +
149A LYS* 2.9 41.6 + - - +
194A PRO* 5.1 4.2 - - + +
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Residues in contact with GLU 146 (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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142A ASN 2.9 19.2 + - - +
143A ALA* 3.8 5.1 - - - +
145A ALA* 1.3 78.0 - - - +
147A ALA* 1.3 61.3 + - - +
149A LYS* 3.4 10.1 + - - +
150A ALA* 3.1 23.6 + - + +
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Residues in contact with ALA 147 (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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107A PRO* 3.2 37.9 - - + +
108A GLU* 4.2 13.0 - - + +
111A GLY* 4.5 2.2 - - - -
143A ALA 3.1 16.3 + - - +
144A TRP 3.7 1.3 - - - +
146A GLU* 1.3 76.5 - - - +
148A ALA* 1.3 63.1 + - - +
150A ALA* 3.3 8.1 + - - +
151A LYS* 3.1 28.6 + - - +
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Residues in contact with ALA 148 (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 GLY* 3.7 23.0 - - - +
114A LEU* 4.6 7.0 - - + -
115A VAL* 3.5 16.8 - - + +
131A PHE* 3.8 20.2 - - + -
144A TRP 2.8 17.0 + - - +
145A ALA* 3.6 4.3 - - - +
147A ALA* 1.3 74.5 - - - +
149A LYS* 1.3 60.2 + - - +
151A LYS* 3.2 2.6 + - - +
152A ILE* 2.9 33.8 + - - +
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Residues in contact with LYS 149 (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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131A PHE* 3.9 33.9 - - + -
133A TYR* 5.0 3.6 + - - -
145A ALA* 2.9 25.4 + - - +
146A GLU* 3.8 8.3 - - - +
148A ALA* 1.3 75.4 - - - +
150A ALA* 1.3 63.6 + - - +
152A ILE* 3.3 9.7 + - - +
153A ALA* 3.0 23.9 + - - +
161A ILE* 4.5 14.6 - - + +
164A THR* 2.8 35.8 + - - +
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Residues in contact with ALA 150 (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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146A GLU* 3.1 15.4 + - + +
147A ALA* 3.6 11.7 - - - +
148A ALA 3.2 0.2 - - - -
149A LYS* 1.3 78.5 - - - +
151A LYS* 1.3 60.7 + - + +
153A ALA* 3.4 7.4 + - - +
154A LYS* 3.3 22.0 + - - +
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Residues in contact with LYS 151 (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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108A GLU* 3.3 43.8 - - - +
111A GLY 4.2 1.3 - - - -
112A GLY* 3.5 25.4 - - - +
115A VAL* 4.3 9.2 - - + -
147A ALA 3.1 16.6 + - - +
148A ALA 3.2 7.2 + - - +
150A ALA* 1.3 76.6 - - + +
152A ILE* 1.3 56.1 + - - +
154A LYS* 3.0 5.0 + - - -
155A GLU* 2.6 61.8 + - - +
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Residues in contact with ILE 152 (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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115A VAL* 3.8 14.6 - - + -
131A PHE* 3.8 21.8 - - + -
148A ALA 2.9 19.6 + - - +
149A LYS* 3.3 6.7 + - - +
151A LYS* 1.3 76.1 - - - +
153A ALA* 1.3 63.6 + - - +
156A HIS* 2.9 38.4 + - - +
159A TRP* 3.7 54.5 - - + +
161A ILE* 3.8 29.2 - - + -
192A ILE* 4.0 8.5 - - + -
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Residues in contact with ALA 153 (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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149A LYS 3.0 16.2 + - - +
150A ALA* 3.7 7.9 - - - +
151A LYS 3.3 0.2 - - - -
152A ILE* 1.3 79.2 - - - +
154A LYS* 1.3 59.4 + - - +
156A HIS 5.0 0.4 - - - -
157A PRO* 4.0 17.9 - - - +
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Residues in contact with LYS 154 (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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150A ALA 3.3 12.7 + - - +
151A LYS* 3.0 5.8 + - - +
153A ALA* 1.3 82.7 - - + +
155A GLU* 1.3 66.4 + - + +
157A PRO* 4.1 7.3 - - - +
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Residues in contact with GLU 155 (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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115A VAL* 4.9 2.4 - - - +
116A ASP* 4.4 14.2 - - - +
151A LYS* 2.6 48.5 + - + +
154A LYS* 1.3 77.5 - - + +
156A HIS* 1.3 88.7 + - + +
157A PRO* 3.4 7.4 - - - +
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Residues in contact with HIS 156 (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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115A VAL* 3.6 31.3 - - + +
116A ASP* 5.6 0.8 + - - -
119A ALA* 4.0 23.4 - - + +
125A GLU 5.7 0.7 - - - -
152A ILE* 2.9 21.0 + - - +
155A GLU* 1.3 106.2 + - + +
157A PRO* 1.3 57.3 - - - +
158A GLY 3.0 5.6 - - - -
159A TRP* 2.9 66.0 + + + +
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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