Contacts of the helix formed by residues 141 - 155 (chain A) in PDB entry 3EUG
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 TRP 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PHE* 4.0 14.4 - + - -
23A THR* 3.4 30.3 - - + +
24A LEU* 3.6 28.3 - - + -
27A VAL* 4.6 1.5 - - + +
44A VAL* 4.0 7.2 - - + -
45A PHE* 3.8 21.3 - + - -
124A THR 3.3 3.1 - - - +
125A VAL* 3.7 31.9 - - + -
126A LEU* 3.5 44.9 - - + +
127A THR* 2.9 40.0 + - + +
136A HIS* 4.0 12.5 - - + +
137A ALA 5.8 0.2 + - - -
139A LEU* 3.4 3.8 - - + -
140A GLY* 1.3 79.7 - - - +
142A GLU* 1.3 58.1 + - - +
144A PHE* 3.1 14.3 + + + +
145A THR* 2.8 30.7 + - - +
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Residues in contact with GLU 142 (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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63A GLN* 4.6 1.9 + - - +
124A THR* 2.7 30.9 + - - -
125A VAL* 3.3 20.2 - - + +
137A ALA* 4.4 13.1 + - + +
139A LEU 4.9 2.7 + - - +
140A GLY 3.4 0.6 - - - -
141A TRP* 1.3 76.7 - - - +
143A THR* 1.3 59.1 + - - +
145A THR* 3.6 2.2 - - - -
146A ASP* 2.8 32.1 + - - +
167A HIS* 3.1 26.5 + - + -
171A LYS* 2.7 37.1 + - - +
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Residues in contact with THR 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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14A GLU* 4.0 1.4 - - - +
19A HIS* 3.5 34.1 - - + +
139A LEU 5.4 0.7 + - - -
140A GLY* 3.4 14.1 + - - -
141A TRP 3.2 0.6 - - - -
142A GLU* 1.3 78.1 - - - +
144A PHE* 1.3 63.6 + - - +
146A ASP* 3.2 11.7 + - + +
147A LYS* 3.1 21.3 + - - +
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Residues in contact with PHE 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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11A LEU* 3.9 28.3 - - + -
14A GLU* 3.2 27.1 + - + +
15A LYS* 4.2 7.0 - - + -
19A HIS* 4.2 1.3 + - - +
20A PHE* 3.5 35.4 - + + -
45A PHE* 4.0 12.8 - + - -
48A PHE* 4.0 16.6 - + - -
126A LEU* 3.9 17.9 - - + -
140A GLY 3.1 13.1 + - - +
141A TRP* 3.1 24.5 + + + +
143A THR* 1.3 77.6 - - - +
145A THR* 1.3 69.8 + - + +
147A LYS* 3.1 6.2 + - - +
148A VAL* 3.0 38.2 + - + +
231A GOL 4.6 5.4 - - - -
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Residues in contact with THR 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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122A LEU* 4.4 18.8 - - + -
123A ASN 3.7 15.7 - - - +
124A THR* 2.7 34.3 + - - +
126A LEU* 4.5 7.9 - - + -
141A TRP 2.8 15.7 + - - +
144A PHE* 1.3 86.0 - - + +
146A ASP* 1.3 65.1 + - - +
148A VAL* 3.6 5.7 - - + +
149A ILE* 3.0 27.9 + - - +
171A LYS* 2.9 26.7 + - - -
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Residues in contact with ASP 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 GLU* 2.8 23.6 + - - +
143A THR* 3.2 11.5 + - + +
145A THR* 1.3 76.0 - - - +
147A LYS* 1.3 59.1 + - - +
149A ILE* 3.2 5.8 + - - +
150A SER* 2.9 29.7 + - - -
171A LYS* 2.7 38.1 + - - +
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Residues in contact with LYS 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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10A VAL 4.9 4.5 - - - -
11A LEU* 4.2 1.8 - - + -
14A GLU* 3.8 36.1 - - + +
143A THR 3.1 9.3 + - - +
144A PHE 3.1 8.3 + - - +
146A ASP* 1.3 82.9 - - - +
148A VAL* 1.3 62.5 + - - +
150A SER* 3.3 14.0 + - - -
151A LEU* 2.9 56.8 + - + +
154A GLN* 5.2 3.4 + - - +
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Residues in contact with VAL 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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7A TRP* 3.9 17.4 - - + -
11A LEU* 4.0 14.8 - - + -
48A PHE* 3.8 36.3 - - + -
120A LEU* 4.7 0.9 - - + -
122A LEU* 3.8 21.5 - - + -
144A PHE* 3.0 36.6 + - + +
145A THR* 3.3 11.9 + - - +
147A LYS* 1.3 74.3 - - - +
149A ILE* 1.3 64.5 + - - +
151A LEU* 3.2 5.9 + - - +
152A ILE* 3.0 30.1 + - + +
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Residues in contact with ILE 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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59A VAL* 5.6 0.4 - - + -
61A LEU* 3.7 23.1 - - + -
122A LEU* 4.3 14.8 - - + -
124A THR* 5.2 0.2 - - + -
145A THR 3.0 17.8 + - - +
146A ASP* 3.7 4.7 - - - +
148A VAL* 1.3 75.8 - - - +
150A SER* 1.3 65.4 + - - +
152A ILE* 3.2 12.3 + - + +
153A ASN* 2.9 22.6 + - + +
161A PHE* 4.6 8.6 - - + -
171A LYS* 3.3 48.2 - - + +
172A GLY* 5.4 0.2 - - - -
174A ILE* 6.3 2.2 - - + -
175A ILE* 4.1 28.7 - - + -
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Residues in contact with SER 150 (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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146A ASP 2.9 17.7 + - - -
147A LYS* 3.5 17.9 + - - -
149A ILE* 1.3 77.9 - - - +
151A LEU* 1.3 61.4 + - - +
153A ASN* 3.2 10.2 + - - +
154A GLN* 3.1 43.3 + - - +
174A ILE* 6.1 6.2 - - - +
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Residues in contact with LEU 151 (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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7A TRP* 5.2 4.3 - - + -
10A VAL* 3.4 42.2 - - + +
11A LEU* 3.6 26.9 - - + -
53A LEU* 5.2 2.0 - - + -
147A LYS* 2.9 45.5 + - + +
148A VAL* 3.2 4.7 + - - +
150A SER* 1.3 72.3 - - - +
152A ILE* 1.3 61.1 + - - +
154A GLN* 4.2 9.2 - - - +
155A HIS* 2.8 62.1 + - + +
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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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7A TRP* 3.6 21.8 - - + -
53A LEU* 4.2 4.7 - - + -
56A VAL* 4.6 6.1 - - + -
59A VAL* 4.0 12.6 - - + -
120A LEU* 3.6 31.4 - - + -
148A VAL* 3.0 22.7 + - + +
149A ILE* 3.7 10.5 - - + +
151A LEU* 1.3 75.5 - - - +
153A ASN* 1.3 65.7 + - - +
156A ARG* 2.9 44.1 + - + +
159A VAL* 4.2 13.9 - - + -
161A PHE* 3.7 22.0 - - + -
180A HIS* 3.7 2.1 - - - +
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Residues in contact with ASN 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 ILE 2.9 13.6 + - - +
150A SER* 3.4 12.5 + - - +
151A LEU 3.2 0.2 - - - -
152A ILE* 1.3 78.8 - - - +
154A GLN* 1.3 66.9 + - - +
161A PHE* 4.8 2.6 - - - -
174A ILE* 4.3 8.7 + - - +
175A ILE* 3.6 15.1 - - + +
176A ASP* 2.8 43.1 + - - +
179A ARG* 3.0 30.3 + - - +
180A HIS* 3.0 23.0 + - - -
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Residues in contact with GLN 154 (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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147A LYS* 5.2 3.9 + - - +
150A SER* 3.1 32.0 + - - +
151A LEU* 3.9 17.3 - - - +
153A ASN* 1.3 88.6 - - - +
155A HIS* 1.3 74.0 + - + +
156A ARG 3.5 0.2 - - - -
157A GLU* 5.0 0.7 - - - +
179A ARG* 3.5 13.9 + - - +
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Residues in contact with HIS 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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5A LEU* 3.3 33.3 - - + +
10A VAL* 3.9 16.0 - - + +
53A LEU* 4.4 15.3 - - + -
151A LEU* 2.8 52.9 + - + +
154A GLN* 1.3 84.4 - - + +
156A ARG* 1.3 68.8 + - + +
157A GLU* 5.3 1.6 - - - +
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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
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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