Contacts of the helix formed by residues 152 - 168 (chain A) in PDB entry 5L04
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 ALA 152 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ASP* 1.3 75.2 - - - +
153A SER* 1.3 63.2 + - - +
155A LEU* 3.3 3.9 + - - +
156A GLU* 3.1 23.1 + - - +
264A HIS* 6.2 1.6 - - + -
267A LYS* 6.0 0.2 - - - -
278B THR* 4.1 15.4 - - - +
279B PHE 3.2 9.4 + - - +
280B GLN* 3.7 28.7 - - - +
281B PRO* 5.4 3.7 - - + +
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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
----------------------------------------------------------
42A LEU* 6.1 0.3 - - - +
68A CYS 3.5 15.3 - - - +
69A ARG* 2.8 39.2 + - - +
70A ILE* 3.5 6.4 - - - +
151A ASP* 3.2 4.8 + - - -
152A ALA* 1.3 80.4 - - - +
154A SER* 1.3 56.9 - - - +
156A GLU* 3.5 7.7 + - - +
157A TYR* 3.0 27.2 + - - +
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Residues in contact with SER 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 3.3 18.1 - - - +
74A CYS* 3.4 17.4 - - - +
78A PHE* 3.5 7.7 - - - -
109A MET* 3.8 18.7 - - - +
150A LEU* 4.2 10.3 - - - -
151A ASP* 2.8 34.1 + - - -
153A SER* 1.3 73.9 - - - +
155A LEU* 1.3 60.8 + - - +
157A TYR* 3.2 2.3 + - - +
158A LEU* 2.9 29.5 + - - +
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TRP* 3.5 20.9 - - + -
150A LEU* 4.4 6.4 - - + +
151A ASP 2.9 5.5 + - - -
152A ALA* 3.6 8.7 - - - +
154A SER* 1.3 74.9 - - - +
156A GLU* 1.3 65.0 + - - +
158A LEU* 3.3 3.4 + - - +
159A PHE* 3.1 21.1 + - - +
264A HIS* 3.8 30.7 - - + +
267A LYS* 3.9 30.5 - - + -
268A VAL* 4.1 8.5 - - + -
271A LEU* 3.4 26.9 - - + -
278B THR* 3.7 24.0 - - + -
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Residues in contact with GLU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.9 21.2 - - + +
152A ALA 3.1 10.8 + - - +
153A SER* 3.7 11.7 - - - +
155A LEU* 1.3 79.4 - - - +
157A TYR* 1.3 62.7 + - - +
159A PHE* 3.5 6.6 + - - +
160A ALA* 3.3 15.6 + - - +
199A HIS* 3.8 13.5 - - - -
203A MET* 4.7 10.6 - - - +
267A LYS* 2.9 40.9 + - - +
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Residues in contact with TYR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 3.4 11.6 - + - -
41A TYR* 3.1 32.7 + + + -
42A LEU* 3.8 31.6 - - + -
68A CYS* 3.8 27.6 - - + -
70A ILE* 4.5 3.1 - - + -
78A PHE* 3.7 26.9 - + + -
107A TYR* 2.5 37.1 + + - -
109A MET* 5.3 0.4 - - + -
153A SER 3.0 18.5 + - - +
154A SER* 3.2 8.0 + - - +
155A LEU 3.2 0.2 - - - -
156A GLU* 1.3 76.8 - - - +
158A LEU* 1.3 64.3 + - - +
160A ALA* 3.3 4.9 + - - +
161A GLN* 3.0 36.2 + - - +
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Residues in contact with LEU 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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109A MET* 4.1 25.8 - - + -
112A TYR* 4.1 20.4 - - + -
116A TRP* 4.0 9.0 - - + -
150A LEU* 4.0 22.0 - - + -
154A SER 2.9 16.0 + - - +
155A LEU* 3.7 5.6 - - - +
156A GLU 3.2 0.4 - - - -
157A TYR* 1.3 82.2 - - - +
159A PHE* 1.3 52.0 + - - +
161A GLN* 3.3 20.7 + - - +
162A GLY* 2.8 30.7 + - - -
271A LEU* 3.6 25.3 - - + +
281A TYR* 3.8 20.6 - - - +
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Residues in contact with PHE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU 3.1 16.5 + - - +
156A GLU* 3.7 9.0 - - - +
158A LEU* 1.3 75.9 - - - +
160A ALA* 1.3 65.0 + - + +
162A GLY* 3.9 0.2 - - - -
163A GLN* 3.0 64.6 + - - +
195A LEU 4.9 1.3 - - - -
196A ALA* 4.6 8.5 - - - -
199A HIS* 3.4 46.0 - + + -
266A LEU* 4.6 1.8 - - + -
267A LYS* 3.7 37.7 - - + -
270A TYR* 3.7 38.4 - + + -
271A LEU* 4.0 8.5 - - + +
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Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 3.3 33.8 - - - +
42A LEU* 4.1 13.5 - - + +
43A SER* 5.4 0.4 - - - +
156A GLU 3.3 9.1 + - - +
157A TYR 3.3 9.2 + - - +
159A PHE* 1.3 81.0 - - + +
161A GLN* 1.3 62.0 + - - +
163A GLN* 3.4 11.1 + - - +
164A TYR* 3.1 22.5 + - - +
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Residues in contact with GLN 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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41A TYR* 3.8 21.4 - - + +
108A ARG* 3.3 45.0 - - - +
109A MET* 2.7 53.8 + - - +
157A TYR* 3.0 22.1 + - - +
158A LEU* 3.5 17.8 - - + +
160A ALA* 1.3 75.3 - - - +
162A GLY* 1.3 61.6 + - - +
164A TYR* 3.4 1.7 + - - +
165A ASP* 2.9 37.1 + - - +
281A TYR* 5.3 2.0 + - - -
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Residues in contact with GLY 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU 2.8 19.6 + - - -
159A PHE 3.4 1.3 + - - -
160A ALA 3.3 0.2 - - - -
161A GLN* 1.3 74.2 - - - +
163A GLN* 1.3 57.2 + - - +
165A ASP* 3.3 6.5 + - - +
166A LEU* 3.0 29.5 + - - +
270A TYR* 4.1 5.8 - - - -
271A LEU* 4.4 2.7 - - - -
274A LEU* 4.0 22.0 - - - +
281A TYR* 4.0 10.1 - - - -
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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 PHE* 3.0 56.2 + - + +
160A ALA* 3.6 9.1 - - - +
162A GLY* 1.3 74.2 - - - +
164A TYR* 1.3 67.5 + - - +
166A LEU* 3.2 1.4 + - - +
167A VAL* 3.1 31.8 + - + +
196A ALA* 3.7 25.3 + - + +
220A TYR* 5.2 5.9 - - - -
270A TYR* 3.4 30.4 - - + +
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Residues in contact with TYR 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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41A TYR* 3.6 28.0 - + + +
83A GLU* 2.7 41.1 + - - -
106A HIS* 4.2 8.0 + - - -
160A ALA 3.1 10.7 + - - +
161A GLN 3.6 7.0 - - - +
163A GLN* 1.3 80.9 - - - +
165A ASP* 1.3 68.1 + - - +
167A VAL* 3.8 2.2 - - - -
168A LYS* 2.9 62.2 + - + +
170A LEU* 4.1 11.4 - - + -
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Residues in contact with ASP 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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108A ARG* 2.7 46.3 + - - -
161A GLN* 2.9 25.9 + - - +
162A GLY* 3.5 7.0 - - - +
163A GLN 3.2 0.2 - - - -
164A TYR* 1.3 79.3 - - - +
166A LEU* 1.3 58.0 + - - +
169A CYS* 3.0 6.8 + - - -
170A LEU* 2.9 31.2 + - - +
171A ALA* 2.9 38.2 + - + +
281A TYR* 4.3 15.4 + - + -
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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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162A GLY 3.0 17.1 + - - +
163A GLN 3.8 3.8 - - - +
165A ASP* 1.3 76.0 - - - +
167A VAL* 1.3 63.0 + - + +
169A CYS* 3.3 8.5 + - - -
171A ALA* 4.1 8.5 - - - +
173A ILE* 4.2 7.9 - - + -
189A CYS* 5.7 1.6 - - - +
192A MET* 3.8 36.1 - - + -
220A TYR 4.6 10.3 - - - +
221A ILE* 5.4 0.2 - - - -
222A PRO* 3.3 46.5 - - + +
270A TYR* 3.3 19.5 - - + +
274A LEU* 4.0 16.6 - - + -
277A LEU* 4.6 5.4 - - + -
278A THR* 4.1 15.9 - - + -
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLN* 3.1 20.0 + - + +
164A TYR* 4.1 2.7 - - - +
166A LEU* 1.3 77.4 - - + +
168A LYS* 1.3 67.3 + - + +
169A CYS 3.2 2.6 + - - -
218A LYS 5.8 0.2 - - - +
219A ARG* 3.7 28.3 - - - +
220A TYR* 3.8 23.1 - - - +
221A ILE 3.6 13.9 - - - +
223A GLU* 3.1 46.8 + - + +
270A TYR* 5.4 1.3 - - - +
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Residues in contact with LYS 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 TYR* 2.9 53.2 + - + +
167A VAL* 1.3 83.0 - - + +
169A CYS* 1.3 71.0 + - - +
170A LEU* 3.1 22.6 + - + +
223A GLU* 3.3 33.7 + - - +
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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