Contacts of the helix formed by residues 232 - 252 (chain A) in PDB entry 3L82
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 SER 232 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LEU* 4.8 0.7 - - - +
179A GLN* 3.4 5.3 - - - +
228A PHE 3.2 15.0 + - - -
229A GLN* 3.9 11.1 + - - -
230A HIS 3.8 0.6 - - - -
231A PHE* 1.3 80.0 - - - +
233A TYR* 1.3 64.5 + - - +
234A ASN* 3.7 10.4 + - - +
235A HIS* 3.1 28.5 + - - +
236A MSE 3.1 20.8 + - - +
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Residues in contact with TYR 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE 3.6 10.2 + - - -
135A GLY* 3.3 26.4 + - - -
136A LYS* 3.5 44.5 + - + +
151A LEU* 4.6 9.0 - - + -
179A GLN* 3.4 31.9 + - + +
183A VAL* 4.1 12.6 - - + -
232A SER* 1.3 74.6 - - - +
234A ASN* 1.3 58.2 + - - +
236A MSE 3.2 30.4 + - + +
237A MSE 2.9 49.0 + - + +
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Residues in contact with ASN 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A SER* 3.2 9.8 - - - +
233A TYR* 1.3 80.8 - - - +
235A HIS* 1.3 58.5 + - + +
237A MSE 3.3 7.6 + - - +
238A GLU* 2.7 56.0 + - - +
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Residues in contact with HIS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 3.8 18.3 - - + +
229A GLN 4.5 7.6 - - - -
230A HIS* 3.8 24.3 + - - -
231A PHE 4.7 1.8 - - - -
232A SER* 3.1 24.9 + - - +
234A ASN* 1.3 76.9 - - + +
236A MSE 1.3 63.9 + - - +
238A GLU* 3.6 23.2 + - - +
239A LYS* 3.4 21.0 + - - +
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Residues in contact with MSE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 4.6 9.4 - - + -
151A LEU* 4.4 13.5 - - + -
172A ILE* 5.4 1.5 - - + +
175A LEU* 4.0 28.4 - - + +
176A ILE* 4.2 23.3 - - + -
179A GLN* 4.1 23.8 - - + -
232A SER 3.1 12.1 + - - +
233A TYR* 3.2 54.3 + - + +
235A HIS* 1.3 78.3 - - - +
237A MSE 1.3 75.2 + - - +
238A GLU 3.4 0.2 + - - -
239A LYS* 3.4 3.6 + - - +
240A ILE* 3.1 35.5 + - + +
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Residues in contact with MSE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 3.9 19.1 - - + -
132A ILE* 3.7 26.9 - - - +
233A TYR* 2.9 41.0 + - + +
234A ASN* 3.6 9.6 - - - +
236A MSE 1.3 84.6 - - + +
238A GLU* 1.3 56.1 + - + +
240A ILE* 3.5 4.5 + - + +
241A LYS* 3.0 68.4 + - + +
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Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ASN* 2.7 41.5 + - - +
235A HIS* 3.9 23.2 - - - +
236A MSE 3.3 0.2 - - - -
237A MSE 1.3 74.1 - - + +
239A LYS* 1.3 69.5 + - + +
241A LYS* 3.2 8.0 + - - +
242A SER* 3.1 20.4 + - - -
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Residues in contact with LYS 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 3.8 20.2 - - + -
171A GLU* 2.7 41.0 + - + +
172A ILE* 3.8 22.2 - - + +
175A LEU* 4.6 15.1 - - + +
235A HIS 3.4 14.4 + - - +
236A MSE 3.8 6.5 - - - +
238A GLU* 1.3 81.8 - - + +
240A ILE* 1.3 62.9 + - - +
242A SER* 2.7 25.6 + - - +
243A TYR 3.2 3.5 + - - -
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Residues in contact with ILE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 4.1 26.9 - - + -
128A PHE* 4.0 33.0 - - + -
129A LEU* 4.9 2.0 - - + -
132A ILE* 4.0 24.9 - - + -
172A ILE* 4.1 29.4 - - + -
176A ILE* 4.8 1.6 - - + -
236A MSE 3.1 38.4 + - + +
237A MSE 3.9 6.1 - - + +
238A GLU 3.3 0.2 - - - -
239A LYS* 1.3 76.7 - - - +
241A LYS* 1.3 57.4 + - - +
243A TYR* 3.2 6.1 + - + +
244A VAL* 3.1 29.0 + - + +
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Residues in contact with LYS 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 3.5 29.9 + - + -
91A ARG* 3.5 34.5 + - + +
93A GLY* 5.3 2.2 - - - +
237A MSE 3.0 49.2 + - + +
238A GLU* 3.7 7.4 - - - +
239A LYS 3.2 0.4 - - - -
240A ILE* 1.3 73.6 - - - +
242A SER* 1.3 61.2 + - - +
244A VAL* 3.7 9.3 + - + +
245A ASN* 3.0 29.7 + - - +
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Residues in contact with SER 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 3.6 19.6 - - - +
238A GLU 3.1 10.8 + - - -
239A LYS* 2.7 23.4 + - - +
241A LYS* 1.3 75.5 - - - +
243A TYR* 1.3 63.3 + - - +
245A ASN* 3.4 13.7 + - - +
246A TYR* 2.9 34.7 - - - -
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Residues in contact with TYR 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 4.1 10.9 + - - -
125A ILE* 3.9 29.1 - - + +
128A PHE* 5.2 8.5 - + - -
129A LEU* 6.0 1.1 - - + -
158A TRP* 3.7 36.8 - + - -
161A ILE* 4.1 17.3 - - + +
164A GLU* 5.8 1.1 - - + -
165A HIS* 4.6 24.7 - + - -
168A LEU* 4.3 15.5 - - + -
172A ILE* 4.1 11.7 - - + -
239A LYS 3.2 6.3 + - - +
240A ILE* 3.2 11.2 + - + +
242A SER* 1.3 81.0 + - - +
244A VAL* 1.3 72.3 + - + +
245A ASN 3.1 0.2 - - - -
246A TYR* 3.0 16.6 + - + +
247A VAL* 3.1 30.9 + - + +
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Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A CYS* 3.8 36.1 - - + +
90A PHE* 4.4 14.1 - - + -
91A ARG* 4.8 9.2 - - + -
125A ILE* 6.5 0.4 - - + -
129A LEU* 4.2 28.7 - - + -
240A ILE* 3.1 17.1 + - + +
241A LYS* 4.0 9.0 - - + +
242A SER 3.4 0.2 - - - -
243A TYR* 1.3 83.3 - - + +
245A ASN* 1.3 59.2 + - - +
247A VAL* 3.3 9.2 + - + +
248A LEU* 3.0 33.2 + - + +
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Residues in contact with ASN 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG* 4.4 15.7 + - - +
241A LYS* 3.0 20.9 + - - +
242A SER* 3.4 12.7 + - - +
243A TYR 3.1 1.0 - - - -
244A VAL* 1.3 76.9 - - - +
246A TYR* 1.3 70.2 + - + +
247A VAL 3.1 0.2 - - - -
248A LEU* 3.4 17.8 + - - +
249A SER* 3.1 23.7 + - - -
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Residues in contact with TYR 246 (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 HIS* 3.1 46.2 - + + +
168A LEU* 5.4 9.2 - - + -
242A SER* 2.9 32.1 - - - -
243A TYR* 3.0 12.0 + + + +
245A ASN* 1.3 82.3 - - + +
247A VAL* 1.3 59.8 + - + +
249A SER* 3.2 19.5 + - - -
250A GLU* 3.5 11.4 + - - +
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Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 6.3 0.2 - - - -
87A CYS* 4.1 22.9 - - - -
121A ARG* 5.8 2.5 - - - +
125A ILE* 4.4 17.0 - - + -
243A TYR* 3.1 46.1 + - + +
244A VAL* 3.6 9.9 - - + +
245A ASN 3.1 0.2 - - - -
246A TYR* 1.3 77.6 - - + +
248A LEU* 1.3 66.6 + - - +
250A GLU* 3.3 9.6 + - - +
251A LYS* 3.0 46.6 + - + +
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Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.4 43.4 - - + +
87A CYS* 3.7 17.9 - - + +
88A ARG* 3.8 13.9 - - + +
91A ARG* 3.4 37.9 - - - +
244A VAL* 3.0 29.0 + - + +
245A ASN* 3.4 15.7 + - - +
247A VAL* 1.3 77.2 - - - +
249A SER* 1.3 61.4 + - - +
252A SER* 3.0 28.1 + - - -
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Residues in contact with SER 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ASN 3.1 13.1 + - - -
246A TYR* 3.2 14.9 + - - -
247A VAL 3.3 0.2 - - - -
248A LEU* 1.3 78.2 - - - +
250A GLU* 1.3 69.1 + - - +
252A SER* 3.5 13.5 + - - -
253A SER* 4.5 2.8 + - - -
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Residues in contact with GLU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 4.3 20.6 + - - -
164A GLU* 5.8 4.5 - - - +
246A TYR 3.5 13.2 + - - +
247A VAL* 3.3 9.5 + - - +
249A SER* 1.3 84.3 + - - +
251A LYS* 1.3 72.2 + - + +
253A SER* 3.1 23.2 + - - -
254A THR* 5.2 0.9 - - - +
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Residues in contact with LYS 251 (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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80A ASP* 2.9 35.0 + - - +
83A CYS* 3.7 36.1 - - + -
84A LEU* 4.3 21.8 - - + +
118A CYS* 6.0 2.4 - - - -
121A ARG* 5.6 5.6 - - - +
122A THR* 3.3 21.9 + - - +
125A ILE* 5.0 5.8 - - - -
247A VAL* 3.0 29.7 + - + +
250A GLU* 1.3 85.1 + - + +
252A SER* 1.3 57.1 + - - +
253A SER 2.8 12.5 + - - -
254A THR* 2.9 36.0 + - + +
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Residues in contact with SER 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 4.3 13.0 - - - +
88A ARG* 4.4 12.8 + - - -
248A LEU 3.0 21.7 + - - -
249A SER* 3.7 10.1 - - - -
250A GLU 3.3 1.6 - - - -
251A LYS* 1.3 75.5 - - - +
253A SER* 1.3 56.6 + - - +
254A THR 3.4 1.8 + - - -
257A MSE 3.9 17.8 - - - +
258A LYS* 4.8 4.3 + - - +
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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
------------------------------------------------------------
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