Contacts of the helix formed by residues 157 - 170 (chain A) in PDB entry 3M6L
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 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A LEU* 3.7 20.3 - - + +
117A GLY* 4.3 0.2 - - - -
153A GLY 3.5 14.5 + - - +
154A ASP 3.4 8.9 + - - +
155A LEU 3.4 0.8 - - - -
156A GLN* 1.3 79.4 - - + +
158A GLY* 1.3 65.7 + - - +
159A ILE* 4.1 16.6 + - + +
160A SER* 2.8 28.9 + - - -
161A TYR* 3.5 3.7 - - - -
5001A TPP 3.3 31.8 + - - +
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Residues in contact with GLY 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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156A GLN 3.5 3.0 + - - -
157A GLU* 1.3 77.4 + - - +
159A ILE* 1.3 62.0 + - - +
161A TYR* 3.1 26.4 + - - +
162A GLU* 3.1 20.8 + - - +
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Residues in contact with ILE 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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116A LEU 4.3 3.1 - - - +
117A GLY* 3.5 31.0 - - - +
118A GLN* 3.9 10.3 - - - +
121A ALA* 3.9 8.1 - - + -
157A GLU* 4.1 9.4 + - + +
158A GLY* 1.3 75.4 - - - +
160A SER* 1.3 61.0 + - - +
162A GLU* 3.4 9.6 + - - +
163A ALA* 3.0 28.2 + - - +
392A HIS* 3.6 55.0 - - + +
393A ALA* 3.7 20.4 - - - +
396A ALA* 3.9 18.8 - - + -
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Residues in contact with SER 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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117A GLY* 5.0 0.7 - - - -
120A VAL* 4.4 19.7 - - - -
154A ASP 3.1 24.0 + - - -
155A LEU* 3.3 18.3 + - - -
157A GLU 2.8 17.8 + - - -
159A ILE* 1.3 79.3 - - - +
161A TYR* 1.3 59.8 + - - +
163A ALA* 3.4 2.0 + - - +
164A CYS* 2.9 37.0 + - - -
201A ARG* 3.1 18.0 + - - -
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Residues in contact with TYR 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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155A LEU 3.4 15.7 + - - -
156A GLN* 3.7 18.2 + - - -
157A GLU 3.5 10.8 - - - -
158A GLY* 3.1 13.5 + - - +
160A SER* 1.3 77.5 + - - +
162A GLU* 1.4 66.4 + - + +
164A CYS* 4.7 0.2 - - - -
165A SER* 3.0 20.3 + - - -
194A PHE* 4.1 3.8 - - - -
196A GLU* 2.6 29.5 + - - -
201A ARG* 3.1 47.1 + - + +
205A GLN* 3.0 22.2 + - - +
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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 GLY 3.1 20.4 + - - +
159A ILE* 3.6 9.5 + - - +
161A TYR* 1.4 78.0 - - + +
163A ALA* 1.3 61.3 + - - +
165A SER* 3.4 5.1 - - - -
166A LEU* 3.3 17.0 + - - +
389A ILE 4.9 2.4 - - - +
390A ARG* 3.5 46.2 - - + +
391A GLU* 4.9 1.2 + - - +
392A HIS* 3.7 10.3 + - - +
393A ALA* 2.9 37.7 + - + +
420A TYR* 5.8 3.3 - - - -
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Residues in contact with ALA 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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120A VAL* 4.7 1.3 - - + -
121A ALA* 3.5 37.7 - - + +
124A VAL* 3.5 25.5 - - + +
159A ILE 3.0 15.1 + - - +
160A SER 3.9 2.9 - - - +
162A GLU* 1.3 75.6 - - - +
164A CYS* 1.3 58.2 + - - +
166A LEU* 3.2 6.4 + - - +
167A ALA 3.1 20.6 + - - -
393A ALA* 4.2 8.3 - - + -
397A ILE* 4.8 3.4 - - + -
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Residues in contact with CYS 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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120A VAL* 3.9 23.1 - - - -
124A VAL* 4.7 4.0 - - - -
160A SER* 2.9 22.4 + - - +
161A TYR* 4.7 0.2 - - - -
163A ALA* 1.3 75.2 - - - +
165A SER* 1.3 65.8 + - - +
167A ALA* 3.0 7.6 + - - +
168A GLY 2.9 20.4 + - - -
175A PHE* 4.8 0.4 - - - -
177A LEU* 4.2 4.7 - - - -
202A PHE* 3.6 26.7 - - + -
205A GLN* 3.4 23.9 - - - +
207A PHE* 3.6 22.5 - - + -
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Residues in contact with SER 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 TYR 3.0 19.0 + - - -
162A GLU* 3.4 8.1 - - - -
164A CYS* 1.3 77.2 - - - +
166A LEU* 1.3 61.9 + - - +
168A GLY* 3.4 1.4 + - - -
169A LEU* 3.2 21.7 + - - +
205A GLN* 3.4 21.3 + - - +
390A ARG* 2.9 28.7 + - - -
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Residues in contact with LEU 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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124A VAL* 4.8 1.1 - - + -
128A MSE 4.7 13.5 - - + -
162A GLU 3.3 3.5 + - - +
163A ALA* 3.2 9.8 + - - +
165A SER* 1.3 78.2 - - - +
167A ALA* 1.3 63.9 + - - +
169A LEU* 3.4 10.7 + - + -
170A HIS* 3.0 53.8 + - + +
172A LEU* 4.7 0.4 - - - +
385A ILE* 6.1 0.2 - - + -
386A HIS 4.0 14.1 - - - +
387A PHE* 3.9 26.2 - - + +
390A ARG* 3.5 35.7 - - + +
393A ALA* 5.2 1.8 - - + -
397A ILE* 3.6 27.4 - - + -
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Residues in contact with ALA 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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124A VAL* 4.0 14.1 - - + +
163A ALA 3.1 12.2 + - - +
164A CYS* 3.0 12.4 + - - +
166A LEU* 1.3 74.9 - - - +
168A GLY* 1.3 57.3 + - - +
171A LYS 3.1 21.8 + - - -
172A LEU* 3.1 37.5 + - + +
175A PHE* 4.3 7.0 - - + -
207A PHE* 4.1 13.0 - - + -
233A PRO* 3.7 7.2 - - + +
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Residues in contact with GLY 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 CYS 2.9 10.9 + - - -
165A SER 3.9 1.3 - - - -
167A ALA* 1.3 76.0 - - - +
169A LEU* 1.3 64.5 + - - +
171A LYS* 3.1 18.5 + - - +
205A GLN 2.9 26.5 - - - -
206A GLY* 4.3 9.4 - - - +
233A PRO* 4.1 10.7 - - - +
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Residues in contact with LEU 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 SER 3.2 13.0 + - - +
166A LEU* 3.7 19.1 - - + +
168A GLY* 1.3 75.4 - - - +
170A HIS* 1.3 83.9 + - + +
171A LYS* 3.5 10.2 + - - +
386A HIS 5.4 3.1 - - - +
390A ARG* 5.3 7.2 - - - +
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Residues in contact with HIS 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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128A MSE 4.0 15.3 - - + +
131A LYS* 5.5 1.6 - - - +
166A LEU* 3.0 44.9 + - + +
169A LEU* 1.3 93.6 + - + +
171A LYS* 1.3 72.1 + - - +
172A LEU* 3.3 24.8 + - + +
379A PHE* 3.8 41.6 - + + -
380A VAL 5.5 0.2 + - - -
385A ILE* 5.7 2.3 - - + +
386A HIS 5.0 5.2 + - - -
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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