Contacts of the helix formed by residues 147 - 161 (chain A) in PDB entry 3UGV
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 SER 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A LYS* 1.3 75.7 - - - +
148A PRO* 1.3 70.6 - - - +
149A ALA* 3.7 5.8 + - - +
150A GLU* 3.0 37.3 + - - +
151A VAL* 2.9 30.6 + - - +
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Residues in contact with PRO 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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146A LYS 4.3 0.2 - - - +
147A SER* 1.3 88.4 - - - +
149A ALA* 1.3 56.4 + - - +
151A VAL* 3.9 0.9 - - - +
152A ALA* 2.8 32.4 + - - +
181A VAL* 3.8 25.1 - - + -
184A GLU* 4.0 26.5 - - + +
185A THR* 3.5 36.6 - - + +
188A ALA* 4.0 13.7 - - + +
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Residues in contact with ALA 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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147A SER* 3.2 6.1 + - - +
148A PRO* 1.3 77.0 - - - +
150A GLU* 1.3 67.7 + - + +
152A ALA* 3.9 5.6 - - - +
153A ALA* 3.1 22.5 + - - +
188A ALA* 5.6 0.7 - - - -
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Residues in contact with GLU 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 LYS* 3.3 41.9 - - + +
147A SER* 3.0 25.6 + - - +
149A ALA* 1.3 75.2 - - + +
151A VAL* 1.3 59.8 + - - +
153A ALA* 3.1 6.5 + - - +
154A GLU* 2.9 29.2 + - - +
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Residues in contact with VAL 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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143A LEU* 3.3 27.5 - - + +
144A TRP 3.5 22.4 - - - +
146A LYS* 3.7 13.0 - - + +
147A SER 2.9 23.7 + - - +
148A PRO 3.9 0.2 - - - +
150A GLU* 1.3 71.3 - - - +
152A ALA* 1.3 58.6 + - - +
154A GLU* 3.2 6.5 + - - -
155A ALA* 2.8 26.2 + - - +
172A LEU* 3.8 14.1 - - + -
176A ARG* 3.7 14.1 - - - +
185A THR* 3.7 23.6 - - + -
189A VAL* 3.8 5.2 - - + -
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Residues in contact with ALA 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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148A PRO 2.8 23.6 + - - +
149A ALA* 3.9 6.1 - - - +
151A VAL* 1.3 74.0 - - - +
153A ALA* 1.3 61.5 + - - +
155A ALA* 3.4 14.0 + - - +
156A VAL* 3.4 13.3 + - - +
188A ALA* 3.8 30.7 - - + +
189A VAL* 4.1 11.6 - - - +
192A ALA* 3.7 10.7 - - + +
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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 ALA 3.1 17.1 + - - +
150A GLU* 3.1 8.2 + - - +
152A ALA* 1.3 72.3 - - - +
154A GLU* 1.3 66.8 + - - +
156A VAL* 3.3 18.9 + - - +
157A GLU* 3.5 15.6 + - - +
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Residues in contact with GLU 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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21A ARG* 3.7 38.0 + - - +
142A GLY* 3.6 4.9 - - - -
143A LEU* 2.7 35.9 + - + -
144A TRP* 4.4 2.8 + - - -
146A LYS* 3.0 30.3 + - - +
150A GLU 2.9 13.0 + - - +
151A VAL* 3.5 8.9 - - - +
153A ALA* 1.3 77.3 - - - +
155A ALA* 1.3 57.9 + - - +
157A GLU* 2.9 17.8 + - - +
158A LEU* 2.8 37.5 + - + +
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Residues in contact with ALA 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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143A LEU* 3.6 13.4 - - + +
151A VAL 2.8 13.6 + - - +
152A ALA 3.4 11.4 - - - +
153A ALA 3.2 0.2 - - - -
154A GLU* 1.3 75.6 - - - +
156A VAL* 1.3 56.2 + - - +
158A LEU* 3.3 3.2 + - - +
159A LYS* 2.9 31.0 + - - +
170A LEU* 4.0 12.7 - - + +
189A VAL* 3.6 31.9 - - + -
193A VAL* 3.8 8.8 - - + +
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Residues in contact with VAL 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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152A ALA 3.7 12.3 - - - +
153A ALA* 3.3 10.9 + - - +
154A GLU 3.2 0.8 - - - -
155A ALA* 1.3 76.0 - - - +
157A GLU* 1.3 63.9 + - + +
159A LYS* 3.8 3.1 - - - +
160A ALA* 3.3 22.2 + - + +
192A ALA* 3.8 29.6 - - + +
193A VAL* 4.0 8.7 - - + -
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Residues in contact with GLU 157 (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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21A ARG* 3.0 30.9 + - - +
153A ALA* 3.5 13.3 + - - +
154A GLU* 2.9 15.8 + - - +
156A VAL* 1.3 75.7 - - + +
158A LEU* 1.3 68.1 + - - +
160A ALA* 3.1 7.3 + - - +
161A GLU* 3.0 24.7 + - + +
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Residues in contact with LEU 158 (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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21A ARG* 3.5 31.0 - - - +
139A ASN* 2.8 32.0 + - - +
141A ASN* 3.9 11.2 - - + -
142A GLY* 4.0 15.5 - - - +
143A LEU* 3.4 42.8 - - + +
154A GLU* 2.8 19.5 + - + +
155A ALA 3.8 3.8 - - - +
157A GLU* 1.3 73.7 - - - +
159A LYS* 1.3 66.1 + - - +
161A GLU* 3.1 25.4 + - - +
167A PHE* 3.3 3.5 - - - -
170A LEU* 3.8 13.5 - - + -
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Residues in contact with LYS 159 (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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155A ALA 2.9 17.2 + - - +
156A VAL 3.8 5.6 - - - +
158A LEU* 1.3 76.3 - - - +
160A ALA* 1.3 58.6 + - - +
162A GLY 2.9 18.0 + - - -
165A THR 3.9 18.8 + - - -
166A GLY* 3.4 4.6 - - - -
167A PHE* 3.0 50.8 + - - +
168A LYS* 4.7 3.2 - - - +
170A LEU* 3.9 12.6 - - + +
193A VAL* 4.0 32.1 - - + +
196A ASP* 4.9 7.5 + - - -
197A THR* 3.2 21.7 + - + +
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Residues in contact with ALA 160 (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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156A VAL* 3.3 11.0 + - + +
157A GLU* 3.1 9.2 + - - +
159A LYS* 1.3 74.1 - - - +
161A GLU* 1.3 63.0 + - - +
162A GLY 2.9 7.3 + - - -
163A GLN* 3.0 21.0 + - - +
164A GLY 6.1 0.9 - - - -
166A GLY* 4.9 4.0 - - - -
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Residues in contact with GLU 161 (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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20A GLN* 4.4 8.7 + - - +
21A ARG* 3.1 29.1 + - - +
139A ASN* 3.0 22.4 + - - +
141A ASN* 3.0 21.4 + - - -
157A GLU 3.0 14.6 + - - +
158A LEU* 3.3 19.1 - - - +
159A LYS 3.1 0.8 - - - -
160A ALA* 1.3 76.4 - - - +
162A GLY* 1.3 59.2 - - - +
163A GLN* 3.3 14.0 + - - +
167A PHE* 3.7 4.0 - - + -
325A TRP* 4.4 8.2 - - + -
327A SER* 4.6 1.7 + - - -
339A LEU* 3.5 18.0 - - - +
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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