Contacts of the helix formed by residues 145 - 156 (chain A) in PDB entry 5YUS
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 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ARG* 3.9 8.1 - - - +
4A ILE* 4.1 10.3 - - - +
143A ALA* 3.8 1.9 - - - +
144A PRO* 1.3 88.1 - - + +
146A LYS* 1.3 66.9 + - - +
147A PHE* 3.7 34.1 - - + -
148A LEU* 4.0 18.2 - - + -
149A ALA* 3.3 19.9 + - - +
228A GLY 3.9 16.2 - - - +
230A ASP* 3.6 26.7 - - + +
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Residues in contact with LYS 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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2A ARG* 5.1 1.2 - - - +
4A ILE* 4.2 11.8 - - + +
98A GLU* 2.7 36.1 + - - -
106A TYR* 3.4 46.6 - - + -
145A VAL* 1.3 75.2 - - - +
147A PHE* 1.3 65.3 + - - +
149A ALA* 3.0 12.1 + - - +
150A LYS 3.1 9.7 + - - -
230A ASP* 3.4 11.5 + - - +
232A ARG* 3.5 42.8 - - + +
233A ASP 3.2 22.4 + - - -
234A VAL* 3.7 15.5 - - + +
235A ASN* 5.5 0.2 - - - +
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Residues in contact with PHE 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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106A TYR* 4.4 4.0 - - - -
145A VAL* 3.7 16.6 - - + -
146A LYS* 1.3 73.7 - - - +
148A LEU* 1.3 85.8 + - + +
150A LYS* 3.5 5.0 + - - +
151A ILE* 3.1 46.3 + - + +
173A LEU* 4.3 1.1 - - + -
176A LEU* 4.6 8.7 - - + -
181A ILE* 4.5 8.7 - - + -
182A PRO* 4.1 18.7 - - + +
225A ARG* 3.2 61.0 - - + +
228A GLY* 4.0 11.9 - - - -
230A ASP* 3.0 28.8 + - + +
232A ARG* 3.8 11.2 - - - +
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Residues in contact with LEU 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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143A ALA* 3.5 15.9 - - + -
144A PRO* 4.7 4.7 - - + -
145A VAL* 3.7 16.1 + - + -
146A LYS 3.2 0.8 - - - -
147A PHE* 1.3 112.2 - - + +
149A ALA* 1.3 59.7 + - - +
151A ILE* 3.5 6.3 + - + +
152A ALA* 2.9 30.7 + - - +
164A ILE* 4.0 8.9 - - + +
169A VAL* 3.9 39.3 - - + -
172A PHE* 3.8 33.0 - - + -
173A LEU* 4.5 5.6 - - + -
176A LEU* 4.7 0.2 - - + -
228A GLY* 4.7 3.6 - - - +
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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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4A ILE* 3.7 30.3 - - + +
6A HIS* 3.6 16.3 - - + +
106A TYR* 4.6 0.2 - - + -
141A GLY* 3.3 22.6 - - - +
143A ALA* 3.4 8.9 - - + +
145A VAL 3.3 10.9 + - - +
146A LYS 3.0 9.0 + - - +
148A LEU* 1.3 77.9 - - - +
150A LYS* 1.3 57.3 + - - +
152A ALA* 3.4 0.6 + - - -
153A SER 3.0 22.7 + - - -
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Residues in contact with LYS 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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6A HIS* 3.2 30.5 + - + +
8A ASP* 3.7 7.5 + - - -
100A LEU* 5.6 0.7 - - + -
104A GLU* 3.3 23.2 + - - -
106A TYR* 3.6 22.7 - - + +
146A LYS 3.1 4.6 + - - +
147A PHE 3.7 8.1 - - - +
148A LEU 3.2 0.2 - - - -
149A ALA* 1.3 74.8 - - - +
151A ILE* 1.3 67.0 + - + +
153A SER* 2.7 22.9 + - - +
154A ASP* 3.6 19.1 + - - +
182A PRO* 3.8 24.7 - - + -
900A TTP 5.9 0.6 + - - -
873C C 3.2 33.4 + - - +
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Residues in contact with ILE 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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147A PHE* 3.1 40.9 + - + +
148A LEU* 3.8 7.4 - - + +
150A LYS* 1.3 74.6 - - + +
152A ALA* 1.3 63.1 + - - +
154A ASP* 3.1 19.6 + - - +
155A MET* 3.5 16.1 - - + +
172A PHE* 3.7 26.7 - - + -
176A LEU* 3.9 30.1 - - + -
180A LYS* 3.5 35.2 - - + +
181A ILE* 4.5 0.9 - - - -
182A PRO* 4.3 5.8 - - + -
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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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140A ALA 3.9 1.7 - - - +
141A GLY* 3.6 9.9 - - - -
142A VAL 4.1 5.2 - - - +
148A LEU 2.9 19.0 + - - +
149A ALA* 3.7 0.4 - - - +
150A LYS 3.2 0.2 - - - -
151A ILE* 1.3 77.1 - - - +
153A SER* 1.3 62.9 + - - +
154A ASP 3.1 0.9 + - - -
155A MET* 3.1 21.4 + - - -
156A ASN 4.3 1.0 + - - -
161A GLN 4.9 0.2 - - - -
162A PHE* 3.5 41.3 + - + +
164A ILE* 4.1 15.7 - - + -
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Residues in contact with SER 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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6A HIS* 3.0 31.6 + - - -
8A ASP* 4.4 7.2 - - - +
139A SER* 3.5 26.5 - - - -
140A ALA* 3.5 9.1 + - - -
141A GLY* 3.4 23.8 - - - +
149A ALA 3.0 7.0 + - - -
150A LYS* 2.7 21.4 + - - +
152A ALA* 1.3 76.1 - - - +
154A ASP* 1.3 62.4 + - - +
155A MET 3.4 0.2 - - - -
156A ASN 4.7 0.7 + - - -
157A LYS* 3.8 6.5 + - - +
160A GLY 5.0 0.3 - - - +
161A GLN* 5.9 0.2 - - - -
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Residues in contact with ASP 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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8A ASP* 5.4 1.7 - - - -
150A LYS* 3.9 25.9 + - - +
151A ILE* 3.1 10.7 + - - +
152A ALA 3.1 1.0 - - - -
153A SER* 1.3 83.4 + - - +
155A MET* 1.3 63.1 + - + +
156A ASN 3.5 0.9 - - - -
157A LYS* 3.6 38.5 + - - +
900A TTP 5.0 2.6 + - - -
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Residues in contact with MET 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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151A ILE* 3.5 20.2 - - + +
152A ALA* 3.1 11.5 + - - +
154A ASP* 1.3 79.5 - - + +
156A ASN* 1.3 65.3 + - - +
157A LYS 3.5 0.9 + - - +
162A PHE* 3.8 44.0 - - + -
172A PHE* 3.6 34.3 - - + -
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Residues in contact with ASN 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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139A SER* 5.0 0.4 - - - -
152A ALA 4.3 3.0 + - - -
153A SER 4.7 0.8 + - - -
155A MET* 1.3 81.1 - - - +
157A LYS* 1.3 60.4 + - - +
158A PRO 3.2 7.8 - - - +
160A GLY* 3.2 23.7 - - - -
161A GLN* 2.7 40.6 + - - +
162A PHE* 4.0 16.9 - - - +
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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