Contacts of the helix formed by residues 153 - 171 (chain A) in PDB entry 3MDR
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 LEU 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A SER* 3.3 13.5 - - - +
150A LEU* 3.0 39.4 + - + +
152A SER* 1.3 80.1 - - - +
154A MET* 1.3 65.4 + - - +
155A GLU 3.0 3.1 - - - -
156A THR* 2.9 21.5 + - - +
157A PHE* 3.0 30.9 + - + -
195A ALA* 3.8 33.4 - - + +
274A ASP* 6.0 2.2 - - + -
275A ILE* 6.3 0.2 - - + -
442A PHE* 3.8 24.7 - - + -
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Residues in contact with MET 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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150A LEU 3.7 0.8 + - - -
151A VAL* 3.3 17.8 + - + +
153A LEU* 1.3 78.1 - - - +
155A GLU* 1.3 56.3 + - - +
157A PHE* 3.5 11.5 + - - +
158A ASN* 2.9 44.5 + - - +
341A TYR* 3.6 12.6 - - + +
342A LEU* 3.1 33.0 - - + +
343A ASP* 4.0 9.4 - - - +
344A PHE* 4.2 21.8 - - + +
347A LEU* 3.8 14.4 - - + -
445A MET* 3.6 28.5 - - + -
449A VAL* 3.8 19.3 - - + -
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Residues in contact with GLU 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 VAL 5.0 0.2 + - - -
152A SER 4.5 9.8 + - - +
153A LEU 3.0 0.6 - - - -
154A MET* 1.3 76.5 - - - +
156A THR* 1.3 61.5 + - - +
158A ASN* 3.3 2.1 + - - +
159A GLU* 2.9 43.7 + - + +
341A TYR* 3.0 36.4 + - - +
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Residues in contact with THR 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 SER 5.2 0.7 + - - -
153A LEU* 2.9 16.3 + - - +
155A GLU* 1.3 78.6 - - - +
157A PHE* 1.3 64.3 + - - +
159A GLU* 3.3 6.7 + - - +
160A LYS* 3.0 31.3 + - + +
191A ILE* 3.8 32.3 - - + +
194A LYS* 3.9 35.6 + - + +
195A ALA* 3.9 15.1 - - + +
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Residues in contact with PHE 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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153A LEU* 3.0 40.6 + - + -
154A MET* 3.8 14.6 - - - +
156A THR* 1.3 76.5 - - - +
158A ASN* 1.3 57.8 + - - +
160A LYS* 4.2 0.7 - - - +
161A ALA* 3.0 32.2 + - - +
191A ILE* 3.4 41.5 - - + +
195A ALA* 4.7 2.9 - - + -
442A PHE* 3.9 29.4 - + - -
445A MET* 3.7 25.4 - - + -
446A GLU* 3.7 38.1 - - + +
449A VAL* 3.6 19.7 - - + +
450A VAL* 5.4 0.3 - - - +
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Residues in contact with ASN 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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154A MET* 2.9 34.7 + - - +
155A GLU 3.7 1.1 - - - +
157A PHE* 1.3 73.9 - - - +
159A GLU* 1.3 67.4 + - - +
161A ALA* 3.4 2.0 + - - +
162A GLU* 2.9 26.8 + - - +
340A ARG 4.0 5.7 - - - +
341A TYR* 3.5 34.0 - - + -
342A LEU* 2.8 53.2 + - - +
449A VAL* 4.1 11.6 - - - +
453A LYS* 4.4 4.2 - - - +
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Residues in contact with GLU 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 GLU* 2.9 28.3 + - + +
156A THR* 3.3 6.7 + - - +
158A ASN* 1.3 76.7 - - - +
160A LYS* 1.3 78.1 + - + +
162A GLU* 3.0 6.6 + - - +
163A GLN* 2.8 31.5 + - + +
194A LYS* 6.1 0.9 - - - -
200A GLU* 4.4 8.8 - - - +
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Residues in contact with LYS 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 THR* 3.0 17.7 + - + +
159A GLU* 1.3 90.0 + - - +
161A ALA* 1.3 60.6 + - - +
163A GLN* 3.4 23.5 + - + +
164A LEU* 2.9 29.6 + - - +
187A THR* 4.1 8.9 - - + +
190A ASP* 3.7 31.6 + - + +
191A ILE* 3.5 36.6 - - + +
194A LYS* 4.8 5.8 - - - -
200A GLU* 2.9 34.2 + - - -
202A SER* 5.3 3.8 + - - +
204A LEU* 3.6 8.6 - - + +
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Residues in contact with ALA 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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157A PHE 3.0 20.3 + - - +
158A ASN 3.8 0.7 - - - +
160A LYS* 1.3 76.9 - - - +
162A GLU* 1.3 59.4 + - - +
164A LEU* 3.3 9.4 + - - +
165A VAL* 3.0 31.5 + - - +
187A THR* 4.7 1.2 - - - +
191A ILE* 5.1 0.4 - - - +
449A VAL* 3.9 11.9 - - + -
450A VAL* 4.2 24.9 - - + -
453A LYS* 3.6 24.7 - - + -
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Residues in contact with GLU 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 ASN 2.9 18.2 + - - +
159A GLU* 3.6 4.3 - - - +
161A ALA* 1.3 75.0 - - - +
163A GLN* 1.3 67.3 + - - +
165A VAL* 3.3 1.9 + - - -
166A GLU* 2.5 50.3 + - - +
340A ARG* 3.0 23.7 + - + +
453A LYS* 2.9 23.3 + - - +
457A ARG* 2.8 42.8 + - - -
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Residues in contact with GLN 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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159A GLU* 2.8 17.6 + - + +
160A LYS* 3.7 23.8 + - - +
162A GLU* 1.3 78.7 - - - +
164A LEU* 1.3 65.0 + - - +
166A GLU* 3.3 8.2 + - - +
167A ILE* 3.2 36.9 + - + +
190A ASP* 4.7 1.6 - - - +
202A SER* 5.7 1.4 - - - -
204A LEU* 3.9 21.2 - - + +
205A LEU* 3.6 37.5 - - + +
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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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160A LYS 2.9 15.4 + - - +
161A ALA* 3.3 10.5 - - - +
163A GLN* 1.3 77.6 - - - +
165A VAL* 1.3 63.0 + - + +
167A ILE* 3.3 3.0 + - - +
168A LEU* 3.1 40.9 + - + +
180A MET* 5.4 0.2 - - + -
183A MET* 4.1 21.5 - - + +
184A LEU* 4.0 12.3 - - + -
187A THR* 3.5 29.4 - - + +
204A LEU* 3.8 17.8 - - + +
450A VAL* 3.8 28.3 - - + -
454A LEU* 4.3 13.7 - - + -
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Residues in contact with VAL 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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161A ALA 3.0 19.8 + - - +
162A GLU* 3.9 5.2 - - - +
163A GLN 3.3 0.4 - - - -
164A LEU* 1.3 77.8 - - + +
166A GLU* 1.3 51.5 + - - +
168A LEU* 3.3 3.5 + - - +
169A GLU* 2.6 42.1 + - - +
450A VAL 5.3 0.2 - - - +
453A LYS* 3.9 26.9 - - + -
454A LEU* 3.8 25.4 - - + -
457A ARG* 3.6 39.0 - - + +
458A LEU* 3.8 15.0 - - + -
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Residues in contact with GLU 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 GLU* 2.5 47.3 + - - +
163A GLN* 3.3 6.9 + - + +
165A VAL* 1.3 72.7 - - - +
167A ILE* 1.3 62.0 + - + +
169A GLU* 3.8 10.2 - - - +
170A ALA* 3.0 27.7 + - - +
340A ARG* 3.3 13.6 + - - +
457A ARG* 3.8 8.1 - - - +
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Residues in contact with ILE 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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163A GLN* 3.2 27.0 + - + +
164A LEU* 3.7 4.9 - - - +
166A GLU* 1.3 75.1 - - + +
168A LEU* 1.3 63.9 + - - +
170A ALA* 3.2 21.2 + - + +
171A LYS* 3.4 26.3 + - + +
183A MET* 3.7 21.1 - - + -
204A LEU* 3.3 48.9 - - + +
205A LEU* 4.4 7.6 - - + -
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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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164A LEU* 3.1 31.2 + - + +
165A VAL 3.6 6.7 - - - +
167A ILE* 1.3 74.6 - - - +
169A GLU* 1.3 64.8 + - - +
171A LYS* 3.0 17.6 + - + +
172A ALA* 3.2 12.8 + - - +
178A VAL* 3.8 27.4 - - + -
180A MET* 3.9 21.5 - - + -
183A MET* 4.0 14.6 - - + -
454A LEU* 3.6 31.0 - - + -
458A LEU* 3.8 8.5 - - + -
460A PHE* 4.3 0.9 - - + -
486A LEU* 3.5 27.8 - - + +
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Residues in contact with GLU 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 VAL* 2.6 25.2 + - + +
166A GLU* 3.8 12.0 - - - +
167A ILE 3.4 0.4 - - - -
168A LEU* 1.3 72.9 - - - +
170A ALA* 1.3 60.9 + - - +
172A ALA* 3.3 21.9 + - + +
457A ARG* 2.8 56.0 + - - +
458A LEU* 3.7 17.0 - - + -
488A PRO* 5.7 7.2 - - + +
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Residues in contact with ALA 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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166A GLU 3.0 13.8 + - - +
167A ILE* 3.2 14.8 - - + +
168A LEU 3.2 0.2 - - - -
169A GLU* 1.3 75.4 - - - +
171A LYS* 1.3 60.1 + - + +
172A ALA 3.8 0.2 + - - -
173A ASP* 5.3 1.0 - - - +
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Residues in contact with LYS 171 (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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167A ILE* 3.4 28.2 + - + +
168A LEU* 3.0 12.0 + - + +
170A ALA* 1.3 80.1 - - + +
172A ALA* 1.3 55.5 + - - +
173A ASP* 2.9 29.4 + - - +
174A GLY 4.4 0.5 + - - -
176A THR* 3.7 24.7 - - + +
178A VAL* 3.7 36.3 - - + -
183A MET* 5.9 4.0 - - + -
486A LEU* 4.6 6.1 + - + +
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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
------------------------------------------------------------
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