Contacts of the helix formed by residues 155 - 169 (chain A) in PDB entry 2MYS
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 ILE 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A TYR* 4.2 13.2 - - + +
123A CYS* 4.3 11.2 - - - -
125A THR* 4.1 11.0 - - - +
135A TYR* 5.5 0.9 - - + +
154A HIS* 1.3 80.5 - - + +
156A PHE* 1.3 83.7 + - + +
157A SER 2.8 1.8 - - - -
158A ILE* 3.2 7.6 + - + +
159A SER* 2.9 21.9 + - - -
177A ILE* 6.2 0.4 - - + -
188A ASN* 3.3 41.3 - - + +
191A ARG* 5.8 3.8 - - + -
192A VAL* 4.4 22.6 - - + +
672A VAL* 4.5 23.8 - - + -
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Residues in contact with PHE 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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134A VAL 3.6 10.1 - - - -
135A TYR* 4.3 22.7 - + + -
139A VAL* 4.2 10.8 - - + -
140A VAL* 3.9 20.2 - - + -
143A TYR* 3.7 21.7 - - + +
154A HIS* 2.9 44.7 - + - -
155A ILE* 1.3 87.9 - - + +
157A SER* 1.3 60.6 + - - +
159A SER* 3.5 5.5 + - - -
160A ASP* 2.7 32.4 + - - +
191A ARG* 4.4 14.4 - - + -
195A TYR* 2.9 47.6 - + + -
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Residues in contact with SER 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 3.2 23.6 + - - -
143A TYR* 4.0 25.8 - - - -
146A LYS 4.3 3.4 + - - -
147A LYS 4.6 0.5 + - - -
148A ARG* 3.4 23.0 + - - +
151A ALA* 4.9 1.2 + - - +
152A PRO 4.7 0.3 + - - -
154A HIS 2.6 20.0 + - - -
156A PHE* 1.3 81.1 - - - +
158A ILE* 1.3 59.8 + - - -
160A ASP* 3.9 1.3 - - - -
161A ASN* 2.7 35.1 + - - +
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Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 3.8 18.4 - - + -
121A LEU 5.0 5.8 - - - +
123A CYS* 3.0 43.5 - - + +
148A ARG* 5.6 2.5 - - - +
154A HIS 3.5 3.2 + - - +
155A ILE* 3.2 8.9 + - + +
157A SER* 1.3 81.8 - - - +
159A SER* 1.3 59.3 + - - +
161A ASN* 3.2 5.8 + - - +
162A ALA* 2.9 28.6 + - - +
175A ILE* 4.0 26.0 - - + -
192A VAL* 6.5 0.7 - - + -
670A HIS* 4.5 19.6 + - + +
671A PHE 4.4 9.6 - - - +
672A VAL* 4.2 14.1 - - + -
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Residues in contact with SER 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ILE* 2.9 17.7 + - - -
156A PHE* 3.5 5.7 + - - -
158A ILE* 1.3 80.7 - - - +
160A ASP* 1.3 61.0 + - - +
162A ALA* 4.0 2.9 - - - -
163A TYR 3.8 2.3 + - - -
175A ILE* 4.8 2.0 - - - -
192A VAL* 4.0 25.6 - - - -
195A TYR* 2.8 35.3 - - - -
196A PHE* 3.1 32.2 - - - -
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Residues in contact with ASP 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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143A TYR 3.4 19.1 - - - +
144A ARG* 2.3 46.5 + - - -
145A GLY* 3.3 7.0 + - - -
146A LYS 4.6 0.7 + - - +
156A PHE 2.7 17.5 + - - +
157A SER 4.0 2.2 - - - +
159A SER* 1.3 75.8 - - - +
161A ASN* 1.3 71.5 + - - +
162A ALA 3.0 1.3 - - - -
163A TYR* 2.9 8.3 + - - +
164A GLN* 2.8 26.2 + - - +
195A TYR* 2.4 33.5 + - - +
199A ILE* 4.1 1.6 - - - +
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Residues in contact with ASN 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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146A LYS 3.2 22.2 + - - -
147A LYS* 3.6 17.6 - - - +
148A ARG* 4.0 13.9 + - - +
157A SER* 2.7 32.1 + - - +
158A ILE* 3.7 5.2 - - - +
160A ASP* 1.3 80.3 - - - +
162A ALA* 1.3 53.9 + - - +
164A GLN* 2.7 23.3 + - - +
165A PHE* 2.8 59.7 + - + +
670A HIS* 5.2 3.4 - - + -
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Residues in contact with ALA 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 ILE 2.9 16.4 + - - +
159A SER* 3.8 9.4 - - - +
161A ASN* 1.3 78.8 - - - +
163A TYR* 1.3 53.2 + - - +
165A PHE* 3.0 4.5 - - - +
166A MET* 2.6 37.4 + - - +
173A GLN* 3.6 27.9 - - + +
175A ILE* 4.5 10.1 - - + -
196A PHE* 4.3 11.0 - - + -
459A ILE* 4.6 1.8 - - + -
670A HIS* 4.1 11.2 + - + -
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Residues in contact with TYR 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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144A ARG* 4.1 30.3 - - - -
159A SER 3.8 7.5 + - - +
160A ASP* 2.9 14.7 + - - +
162A ALA* 1.3 77.2 - - - +
164A GLN* 1.3 70.6 + - - +
166A MET* 2.9 30.7 + - - +
167A LEU* 3.0 29.1 + - + +
196A PHE* 4.0 18.6 - + + -
199A ILE* 4.5 13.5 - - + -
200A ALA* 3.1 24.3 - - + +
254A PHE* 4.1 14.6 - + - -
258A GLY* 2.4 38.4 + - - -
259A LYS* 4.4 6.6 + - - -
459A ILE* 4.3 5.1 - - + +
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Residues in contact with GLN 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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144A ARG* 4.3 8.1 - - - +
145A GLY* 4.2 16.7 - - - +
146A LYS 4.1 4.6 + - - -
147A LYS* 3.0 32.8 - - - +
160A ASP* 2.8 26.4 + - - +
161A ASN* 2.7 46.1 + - - +
163A TYR* 1.3 71.7 - - - +
165A PHE* 1.3 57.3 + - + +
166A MET 2.7 0.5 + - - -
167A LEU* 2.6 36.4 + - - +
168A THR* 2.8 19.1 + - - +
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Residues in contact with PHE 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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147A LYS* 6.2 4.0 - - + -
161A ASN* 2.8 43.0 + - + +
162A ALA 3.0 5.4 - - - +
164A GLN* 1.3 79.5 - - + +
166A MET* 1.3 66.3 + - - +
168A THR* 3.7 7.6 + - + -
169A ASP* 2.9 52.1 + - - +
170A ARG 3.9 0.2 + - - -
171A GLU 4.6 0.2 + - - -
173A GLN* 3.6 16.8 + - - +
668A HIS* 4.6 12.6 - + - -
670A HIS* 3.9 24.0 - + - -
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Residues in contact with MET 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 ALA 2.6 18.0 + - - +
163A TYR* 3.0 24.9 - - - +
164A GLN 2.7 1.0 + - - -
165A PHE* 1.3 80.2 - - - +
167A LEU* 1.3 59.5 + - - -
170A ARG* 3.0 24.4 + - - -
171A GLU 3.7 13.2 + - - +
173A GLN* 3.6 11.4 - - - +
254A PHE* 3.0 52.9 - - + -
457A TYR* 3.6 41.5 - - + -
458A PHE 3.6 12.8 - - - +
459A ILE* 3.7 11.2 - - + -
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Residues in contact with LEU 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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144A ARG* 5.5 3.1 - - - +
163A TYR* 3.0 43.9 + - + +
164A GLN* 2.6 13.3 + - - +
166A MET* 1.3 79.3 - - + +
168A THR* 1.3 61.0 + - - +
170A ARG* 4.0 12.4 + - - +
256A ALA 5.0 1.1 - - - +
257A THR 3.7 9.6 - - - +
258A GLY* 3.6 31.2 - - - -
457A TYR* 4.9 18.3 + - + +
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Residues in contact with THR 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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164A GLN* 2.8 26.3 + - - +
165A PHE* 4.1 7.6 - - + -
167A LEU* 1.3 75.5 - - - +
169A ASP* 1.3 74.8 + - - +
170A ARG* 4.5 3.8 - - - +
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Residues in contact with ASP 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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165A PHE* 2.9 41.2 + - - +
168A THR* 1.3 92.9 - - - +
170A ARG* 1.3 74.4 + - - +
171A GLU* 3.3 29.8 + - + +
173A GLN* 5.2 0.4 - - - +
668A HIS* 4.7 6.2 + - - -
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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