Contacts of the helix formed by residues 243 - 262 (chain A) in PDB entry 4IA4
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 TRP 243 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LYS* 3.2 35.9 - - + +
162A GLY* 6.5 0.2 - - - -
165A LEU* 3.9 35.0 - - + -
239A TRP 4.7 0.4 + - - -
240A ASP 3.4 20.3 + - - +
241A ASP 2.7 9.6 + - - -
242A GLN* 1.3 75.1 - - - +
244A ILE* 1.3 74.6 + - + +
246A TRP* 3.2 6.4 + - - +
247A VAL* 2.9 58.5 + - + +
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Residues in contact with ILE 244 (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 VAL* 3.3 33.9 - - + -
161A LYS* 4.3 16.2 - - + +
164A ALA* 3.8 14.8 - - + +
165A LEU* 3.6 34.5 - - + +
168A GLU* 4.2 9.1 - - + +
241A ASP* 3.0 20.4 - - + +
243A TRP* 1.3 102.8 - - + +
245A PHE* 1.3 65.4 + - + +
248A GLY* 2.7 33.1 + - - -
249A PRO* 3.6 0.5 - - - +
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Residues in contact with PHE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASN* 3.3 44.6 - - + -
154A SER* 3.7 15.7 - - - -
155A VAL 4.7 0.7 - - - -
168A GLU* 3.7 25.6 - - + +
217A THR* 3.6 32.3 - - + -
220A GLY* 4.6 1.1 - - - -
222A ASN 5.8 0.2 - - - -
223A PRO* 3.6 17.5 - - - +
226A SER* 3.2 29.2 - - - +
241A ASP* 4.0 20.2 - - + -
242A GLN* 4.1 17.7 - - - +
243A TRP 3.3 0.8 - - - -
244A ILE* 1.3 82.0 - - + +
246A TRP* 1.3 59.3 + - + +
249A PRO* 3.3 23.5 - - + +
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Residues in contact with TRP 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO* 5.6 2.7 - - + -
123A MET* 6.3 0.9 - - - -
127A CYS* 4.1 17.9 - - - -
223A PRO* 4.0 17.6 + - + -
227A PHE* 3.7 37.6 - + + +
242A GLN* 3.2 43.3 + - + +
243A TRP* 3.2 8.0 + - - +
244A ILE 3.1 0.6 - - - -
245A PHE* 1.3 85.7 - - + +
247A VAL* 1.3 66.7 + - + +
248A GLY 3.4 0.4 - - - -
249A PRO* 4.1 0.6 - - - +
250A PHE* 2.9 63.0 + + - +
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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
----------------------------------------------------------
165A LEU* 3.8 15.9 - - + -
243A TRP* 2.9 43.3 + - + +
246A TRP* 1.3 79.1 - - + +
248A GLY* 1.3 69.0 + - - +
250A PHE* 4.2 1.9 - - - +
251A ILE* 3.2 41.5 + - + +
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Residues in contact with GLY 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 3.5 15.2 - - - +
168A GLU* 4.1 5.4 - - - -
169A ILE* 3.6 18.0 - - - +
244A ILE 2.7 19.3 + - - -
247A VAL* 1.3 72.7 - - - +
249A PRO* 1.3 69.6 - - - +
251A ILE* 2.9 6.9 + - - +
252A GLY* 2.9 19.2 + - - -
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Residues in contact with PRO 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA* 3.8 20.6 - - + -
168A GLU* 4.1 7.9 - - + +
172A THR* 3.3 27.0 - - + +
221A ILE* 3.8 20.0 - - - +
222A ASN 4.0 4.3 - - - +
223A PRO* 3.8 13.0 - - + -
244A ILE 3.6 2.2 - - - +
245A PHE* 3.3 30.5 - - + +
246A TRP 4.1 0.7 - - - +
248A GLY* 1.3 86.4 - - - +
250A PHE* 1.3 52.3 + - - +
252A GLY 3.1 1.0 + - - -
253A ALA* 2.6 37.1 + - - +
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Residues in contact with PHE 250 (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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102A PRO* 4.1 18.8 - - + -
103A ALA* 4.9 2.2 - - - -
106A PHE* 3.2 60.9 - + + -
123A MET* 4.3 13.9 - - - -
223A PRO* 3.4 26.7 - - + -
246A TRP* 2.9 50.0 + + - +
247A VAL* 4.2 2.5 - - - +
248A GLY 3.2 1.2 - - - -
249A PRO* 1.3 78.6 - - - +
251A ILE* 1.3 59.0 + - + +
253A ALA* 4.1 2.2 - - - -
254A ALA* 2.9 29.5 + - - +
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Residues in contact with ILE 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 5.4 2.2 - - + -
169A ILE* 3.4 36.6 - - + -
247A VAL* 3.2 33.6 + - + +
248A GLY 2.9 9.2 + - - +
250A PHE* 1.3 76.7 - - + +
252A GLY* 1.3 67.1 + - - +
254A ALA* 3.3 5.3 + - - +
255A VAL* 2.9 37.0 + - + +
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Residues in contact with GLY 252 (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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169A ILE* 3.4 30.3 - - - +
172A THR* 4.3 3.4 - - - -
173A PHE* 4.3 9.6 - - - -
248A GLY 2.9 11.2 + - - -
249A PRO 3.5 2.9 - - - -
251A ILE* 1.3 78.1 - - - +
253A ALA* 1.3 63.2 + - - +
255A VAL* 3.0 6.0 + - - +
256A ALA* 2.8 26.0 + - - +
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Residues in contact with ALA 253 (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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103A ALA* 3.1 32.3 - - - +
106A PHE* 4.0 5.6 - - + -
107A GLY* 4.0 11.0 - - - +
172A THR* 4.1 2.2 - - - +
176A VAL* 3.4 25.5 - - + +
249A PRO 2.6 20.2 + - - +
250A PHE 3.6 4.3 - - - +
252A GLY* 1.3 69.4 - - - +
254A ALA* 1.3 57.0 + - - +
256A ALA* 3.5 2.6 - - - +
257A ALA* 3.1 27.5 + - - +
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Residues in contact with ALA 254 (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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106A PHE* 3.9 5.3 - - + -
110A LEU* 3.5 28.8 - - + +
250A PHE 2.9 18.8 + - - +
251A ILE* 3.6 5.4 - - - +
253A ALA* 1.3 73.9 - - - +
255A VAL* 1.3 67.5 + - + +
257A ALA* 3.1 5.0 + - - +
258A ALA* 2.9 22.1 + - - +
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Residues in contact with VAL 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ILE* 4.9 5.6 - - + -
173A PHE* 3.8 20.2 - - + -
251A ILE* 2.9 42.3 + - + +
252A GLY* 3.5 7.2 - - - +
254A ALA* 1.3 71.6 - - + +
256A ALA* 1.3 69.0 + - - +
258A ALA* 3.0 10.0 + - + +
259A TYR* 2.9 18.2 + - + +
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Residues in contact with ALA 256 (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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173A PHE* 3.5 23.5 - - + +
176A VAL* 3.2 36.8 - - + -
177A TYR* 3.9 13.9 - - - +
180A PHE* 4.4 2.7 - - - -
252A GLY 2.8 16.5 + - - +
253A ALA 3.5 0.2 - - - +
255A VAL* 1.3 71.8 - - - +
257A ALA* 1.3 56.0 + - - +
259A TYR* 2.7 25.7 + - - +
260A HIS* 2.8 14.0 + - - +
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Residues in contact with ALA 257 (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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107A GLY 4.0 9.4 - - - +
110A LEU* 4.5 13.2 - - + -
111A ALA 5.3 1.1 - - - +
180A PHE* 3.5 29.1 - - + -
253A ALA 3.1 10.8 + - - +
254A ALA* 3.1 13.4 + - - +
256A ALA* 1.3 79.5 - - - +
258A ALA* 1.3 57.5 + - - +
261A GLN* 2.8 39.4 + - + +
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Residues in contact with ALA 258 (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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254A ALA 2.9 12.0 + - - +
255A VAL* 3.0 10.3 + - + +
257A ALA* 1.3 74.2 - - - +
259A TYR* 1.3 66.8 + - - +
261A GLN* 5.0 0.9 - - - -
262A TYR* 3.0 35.2 + - + +
263A VAL* 3.2 6.2 + - + +
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Residues in contact with TYR 259 (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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173A PHE* 3.6 24.9 - + + -
177A TYR* 3.7 44.5 + + + -
255A VAL* 2.9 11.1 + - + +
256A ALA 2.7 13.5 + - - +
258A ALA* 1.3 73.0 - - - +
260A HIS* 1.3 59.5 + - - +
263A VAL* 3.3 36.9 - - + +
264A LEU* 3.0 39.2 + - + +
42C ILE* 4.0 16.2 - - + -
43C ALA* 3.4 23.2 + - - +
46C ILE* 3.2 38.1 - - + +
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Residues in contact with HIS 260 (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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113A LYS* 5.9 3.1 - - - -
177A TYR* 4.7 15.5 - + + -
180A PHE* 3.2 56.6 + + + -
181A SER* 4.4 10.8 - - - -
183A THR* 5.8 2.0 - - + -
256A ALA 2.8 13.1 + - - +
257A ALA 4.2 0.9 - - - +
259A TYR* 1.3 78.8 - - - +
261A GLN* 1.3 92.0 + - - +
264A LEU* 3.5 11.6 - - + -
265A ARG* 3.1 64.4 - - + +
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Residues in contact with GLN 261 (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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111A ALA* 3.9 34.8 - - + +
113A LYS* 4.6 13.3 - - - +
180A PHE* 3.9 12.3 - - + -
257A ALA* 2.8 26.7 + - + +
258A ALA* 5.0 0.9 - - - -
260A HIS* 1.3 111.2 + - - +
262A TYR* 1.3 63.2 + - + +
264A LEU 3.7 8.0 - - - +
265A ARG* 5.0 3.9 - - - +
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Residues in contact with TYR 262 (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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258A ALA* 3.0 20.8 + - + +
261A GLN* 1.3 80.4 - - - +
263A VAL* 1.3 77.8 + - + +
264A LEU 3.3 8.8 + - - +
39C ARG* 4.8 3.8 + - - -
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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