Contacts of the helix formed by residues 158 - 170 (chain A) in PDB entry 5UWS
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 GLU 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A HIS* 4.1 7.4 - - - -
154A ASN 4.6 0.2 - - - +
156A ASN* 3.5 4.6 + - - -
157A PHE* 1.3 94.8 + - + +
159A LYS* 1.3 95.0 + - + +
160A PRO* 3.3 2.2 - - - -
161A PHE* 3.2 6.6 + - - +
162A LEU* 3.1 24.7 + - + +
176A PHE* 3.9 24.1 - - + -
130B LYS* 3.8 42.2 + - + +
131B THR* 4.3 9.4 - - + -
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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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147A TYR* 3.7 36.3 + - + +
156A ASN* 2.9 50.1 + - + +
158A GLU* 1.3 99.5 - - + +
160A PRO* 1.3 67.4 - - + +
162A LEU* 3.3 14.7 + - + +
163A TRP* 3.0 26.5 + - - +
130B LYS* 6.0 1.1 - - - +
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Residues in contact with PRO 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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26A PHE* 4.1 14.8 - - + -
87A ILE* 4.0 23.3 - - + -
118A VAL* 3.9 13.7 - - + +
120A CYS* 3.7 22.9 - - - -
147A TYR* 4.0 13.9 - - + -
149A ILE* 4.4 5.2 - - + -
156A ASN 3.2 13.7 - - - +
157A PHE 3.6 7.0 - - - +
158A GLU 3.4 4.3 - - - -
159A LYS* 1.3 91.5 - - + +
161A PHE* 1.3 56.2 + - + +
163A TRP* 4.0 0.2 - - - +
164A LEU* 3.2 35.4 + - - +
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Residues in contact with PHE 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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13A LEU* 3.6 27.4 - - + -
26A PHE* 3.5 36.8 - + - -
27A VAL* 5.8 3.6 - - + -
30A HIS* 3.6 31.9 - + - -
50A LEU* 3.5 22.7 - - + -
52A PHE* 3.7 27.4 - + + -
61A PHE* 3.9 21.3 - + + -
63A VAL* 4.3 11.2 - - + -
87A ILE* 4.5 6.1 - - + -
157A PHE 4.4 1.8 - - - -
158A GLU 3.2 6.0 + - - +
160A PRO* 1.3 76.7 - - + +
162A LEU* 1.3 61.5 + - - +
164A LEU* 4.6 2.5 - - - -
165A ALA* 2.8 31.2 + - - +
176A PHE* 4.0 5.6 - - + -
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Residues in contact with LEU 162 (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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158A GLU* 3.1 20.3 + - + +
159A LYS* 3.3 17.0 + - + +
161A PHE* 1.3 77.9 - - - +
163A TRP* 1.3 62.3 + - - +
165A ALA* 3.2 3.3 + - - +
166A ARG* 3.0 57.6 + - - +
174A LEU* 3.9 35.2 - - + +
175A GLU* 4.3 6.3 - - - +
176A PHE* 3.6 35.7 - - + +
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Residues in contact with TRP 163 (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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116A PRO* 3.7 16.4 - - + -
117A ILE 3.7 20.2 - - - -
118A VAL* 3.4 17.7 - - + -
143A ASN 5.0 7.4 - - - -
144A LEU 5.4 0.2 - - - -
145A GLN* 3.1 41.2 + - + -
147A TYR* 3.6 20.2 - - + +
159A LYS 3.0 16.8 + - - +
160A PRO 4.0 2.0 - - - +
162A LEU* 1.3 78.1 - - - +
164A LEU* 1.3 87.3 + - + +
166A ARG* 3.2 14.9 + - + +
167A LYS* 3.0 57.9 + - + +
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Residues in contact with LEU 164 (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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13A LEU* 3.7 30.1 - - + -
61A PHE* 4.2 11.2 - - + -
85A CYS* 3.9 10.3 - - + -
86A ALA 4.2 4.0 - - - +
87A ILE* 4.1 12.3 - - + -
116A PRO* 3.6 26.9 - - + +
118A VAL* 3.7 14.6 - - + -
160A PRO 3.2 20.2 + - - +
161A PHE* 4.0 4.5 - - - +
163A TRP* 1.3 97.8 - - + +
165A ALA* 1.3 61.0 + - - +
167A LYS* 3.1 3.5 + - - +
168A LEU* 2.8 38.8 + - + +
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Residues in contact with ALA 165 (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 ILE* 4.0 32.5 - - + -
61A PHE* 4.0 5.3 - - + -
161A PHE 2.8 20.2 + - - +
162A LEU* 3.2 7.4 + - - +
164A LEU* 1.3 75.7 - - - +
166A ARG* 1.3 56.3 + - - +
169A ILE* 3.0 37.3 + - - +
174A LEU* 4.1 22.2 - - + -
176A PHE* 4.9 3.8 - - + -
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Residues in contact with ARG 166 (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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162A LEU* 3.0 41.8 + - - +
163A TRP* 3.6 14.3 - - + +
165A ALA* 1.3 75.9 - - - +
167A LYS* 1.3 61.1 + - + +
170A GLY* 2.9 23.9 + - - -
171A ASP 3.2 28.6 + - - +
172A PRO* 3.3 26.8 + - + -
173A ASN 4.9 0.8 - - - -
174A LEU* 2.8 36.3 + - + +
175A GLU* 3.3 27.3 + - - -
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Residues in contact with LYS 167 (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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116A PRO* 4.0 21.1 - - + -
163A TRP* 3.0 63.8 + - + +
164A LEU 3.1 6.7 + - - +
166A ARG* 1.3 80.5 - - + +
168A LEU* 1.3 63.0 + - - +
170A GLY* 3.5 10.3 + - - -
172A PRO* 6.3 1.0 - - - +
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Residues in contact with LEU 168 (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 PHE* 3.8 52.3 - - + -
59A ILE* 4.7 0.2 - - + -
61A PHE* 3.6 31.0 - - + -
84A GLN* 3.5 28.7 - - + +
85A CYS* 3.9 12.3 - - + -
116A PRO* 4.2 14.1 - - + -
164A LEU 2.8 26.1 + - - +
165A ALA* 4.1 2.9 - - - +
167A LYS* 1.3 74.2 - - - +
169A ILE* 1.3 62.7 + - - +
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Residues in contact with ILE 169 (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 VAL* 5.2 7.9 - - + -
11A PHE* 3.9 28.9 - - + -
56A ARG* 4.1 33.2 + - + +
59A ILE* 4.0 15.3 - - + -
165A ALA 3.0 17.9 + - - +
166A ARG 4.9 0.2 - - - -
168A LEU* 1.3 76.6 - - - +
170A GLY* 1.3 60.6 + - - +
171A ASP* 4.3 6.7 - - + +
174A LEU* 3.9 21.5 - - + -
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Residues in contact with GLY 170 (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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56A ARG* 5.6 0.4 - - - -
166A ARG 2.9 10.9 + - - -
167A LYS* 3.5 6.8 + - - -
168A LEU 3.4 2.8 - - - -
169A ILE* 1.3 79.2 - - - +
171A ASP* 1.3 58.9 + - - +
172A PRO* 4.0 7.2 - - - +
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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