Contacts of the helix formed by residues 244 - 259 (chain A) in PDB entry 3T79
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 ARG 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A GLN* 3.6 38.1 - - - +
242A TYR 3.1 22.4 + - - -
243A PRO* 1.3 74.9 - - - +
245A GLU* 1.3 71.6 + - - +
246A LEU* 4.8 10.1 - - + -
247A THR* 2.0 35.4 + - + -
248A LEU* 3.5 4.3 - - - +
6C T 3.1 44.9 + - + +
7C T 2.5 40.6 + - - +
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Residues in contact with GLU 245 (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 PHE* 3.0 47.2 - - + -
157A THR* 4.9 0.3 - - - +
243A PRO 5.1 0.3 - - - +
244A ARG* 1.3 80.0 - - - +
246A LEU* 1.3 71.4 + - - +
247A THR 3.0 1.8 - - - -
248A LEU* 2.8 18.2 + - - +
249A GLY 2.9 8.8 + - - -
265A LYS* 5.5 4.9 - - - +
269A PHE* 3.7 12.3 - - + -
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Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ARG* 4.8 8.5 - - + -
245A GLU* 1.3 79.2 + - - +
247A THR* 1.3 95.5 + - + +
249A GLY* 2.8 15.3 + - - +
250A ASN* 2.8 14.2 + - - +
265A LYS* 5.7 4.9 - - - +
7B T 5.4 13.9 - - + -
8B A 5.9 1.6 - - - +
6C T 4.3 6.7 - - + -
7C T 3.6 35.0 - - + -
8C A 4.6 13.5 - - - +
9C T 5.4 2.5 - - + +
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Residues in contact with THR 247 (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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243A PRO* 4.0 4.9 - - - +
244A ARG* 2.0 38.6 + - + +
246A LEU* 1.3 101.2 - - + +
248A LEU* 1.3 63.8 + - - +
250A ASN* 3.0 6.6 + - - +
251A TRP* 2.8 41.7 + - - +
5C T 3.7 24.2 - - + +
6C T 2.9 31.0 - - + +
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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
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139A LEU* 4.9 13.2 - - + -
142A ASP* 5.0 11.2 - - - +
153A PHE* 2.9 43.3 - - + -
156A ARG* 5.5 0.2 - - - +
234A ILE* 4.7 10.5 - - + -
242A TYR* 4.5 9.0 - - + -
243A PRO* 4.0 25.1 - - + +
244A ARG 3.5 11.7 - - - +
245A GLU 2.8 6.9 + - - +
247A THR* 1.3 74.8 + - - +
249A GLY* 1.3 57.1 + - - +
250A ASN 2.9 4.0 - - - -
251A TRP* 2.7 37.0 + - + +
252A TYR* 2.8 21.4 + - + +
269A PHE* 3.7 13.0 - - + -
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Residues in contact with GLY 249 (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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245A GLU 2.9 8.0 + - - -
246A LEU* 2.8 13.2 + - - -
248A LEU* 1.3 71.9 - - - +
250A ASN* 1.3 50.9 + - - +
252A TYR* 4.6 0.2 - - - -
253A PRO* 2.7 28.8 - - - +
263A TYR* 3.9 9.3 + - - -
265A LYS* 4.3 11.8 - - - +
269A PHE* 3.3 20.7 - - - -
7B T 5.2 6.6 + - - -
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Residues in contact with ASN 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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129A HIS* 3.9 23.1 + - - -
246A LEU 2.8 9.4 + - - +
247A THR* 3.2 12.6 - - - +
248A LEU 2.8 0.2 + - - -
249A GLY* 1.3 74.5 - - - +
251A TRP* 1.3 59.8 + - + +
252A TYR 3.1 1.3 - - - -
253A PRO* 3.0 12.6 - - - +
254A THR* 2.5 35.5 + - - -
9B T 6.2 2.4 - - - +
5C T 5.8 1.2 + - - -
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Residues in contact with TRP 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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129A HIS* 3.5 31.3 - + + -
130A PHE* 3.2 42.5 - + + -
135A ASP* 3.6 35.2 - - + -
138A LYS* 3.9 28.0 - - + -
139A LEU* 3.7 23.3 - - + -
243A PRO* 6.5 1.6 - - + -
247A THR* 2.8 38.5 + - - +
248A LEU* 2.7 23.6 + - + +
250A ASN* 1.3 73.9 - - + +
252A TYR* 1.3 61.1 + - - +
254A THR* 3.3 19.1 - - - -
255A ILE* 3.3 7.3 + - - +
5C T 3.5 37.9 + - - -
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Residues in contact with TYR 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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139A LEU* 3.8 20.6 - - + -
142A ASP* 2.9 26.6 + - - -
143A PHE* 2.7 50.7 - + + +
156A ARG* 4.7 0.8 + - - -
248A LEU* 2.8 23.0 + - + +
251A TRP* 1.3 73.3 - - - +
253A PRO* 1.3 73.8 - - + +
255A ILE* 2.9 27.9 - - + +
256A PHE* 3.1 27.5 + + - -
263A TYR* 3.6 22.4 - + + +
268A TRP* 4.1 23.6 - + + +
269A PHE* 3.7 22.7 - + - -
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Residues in contact with PRO 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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249A GLY 2.7 30.5 - - - +
250A ASN* 3.0 19.7 - - - +
252A TYR* 1.3 87.0 - - + +
254A THR* 1.3 52.1 + - - +
256A PHE* 3.7 7.8 - - + +
257A LYS* 2.8 54.5 + - + +
263A TYR* 4.1 25.5 - - + -
7B T 5.4 3.1 - - - +
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Residues in contact with THR 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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125A LEU* 5.7 6.0 - - + +
127A SER* 3.2 34.8 - - - +
129A HIS* 4.4 5.4 - - + +
130A PHE* 4.3 13.0 - - + -
250A ASN* 2.5 33.1 + - - -
251A TRP* 3.3 10.5 - - - -
252A TYR 3.1 0.2 - - - -
253A PRO* 1.3 79.1 - - - +
255A ILE* 1.3 59.2 + - - +
257A LYS* 3.9 16.7 + - - +
258A TYR* 3.4 19.8 + - - +
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Residues in contact with ILE 255 (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 ILE* 4.3 7.9 - - + -
116A ASN* 5.0 4.5 - - + +
117A LEU* 3.8 35.9 - - + -
125A LEU* 5.4 6.7 - - + -
130A PHE* 4.6 6.0 - - + -
139A LEU* 3.8 18.6 - - + -
143A PHE* 6.4 0.7 - - + -
251A TRP 3.3 8.9 + - - +
252A TYR* 2.9 27.4 - - + +
254A THR* 1.3 80.6 - - - +
256A PHE* 1.3 64.3 + - + +
258A TYR* 3.1 16.3 + - + -
259A CYS* 2.8 52.2 + - - -
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Residues in contact with PHE 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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109A ILE* 4.4 14.4 - - + -
113A ILE* 4.4 17.0 - - + -
143A PHE* 4.6 1.8 - + - -
252A TYR* 3.1 40.6 + + - +
253A PRO 3.7 3.4 - - - +
255A ILE* 1.3 79.8 - - + +
257A LYS* 1.3 57.0 + - - +
259A CYS* 3.6 4.6 - - - +
260A GLN 2.8 10.4 + - - -
261A LEU* 2.7 65.3 + - + +
262A PRO 3.3 15.7 - - - -
263A TYR* 3.8 21.8 - + + -
268A TRP* 2.9 46.0 - + - -
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Residues in contact with LYS 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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253A PRO* 2.8 45.5 + - + +
254A THR* 3.9 14.5 + - - +
256A PHE* 1.3 73.6 - - - +
258A TYR* 1.3 60.1 - - - +
260A GLN* 2.5 33.6 + - - +
261A LEU 5.1 0.2 - - - -
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Residues in contact with TYR 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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116A ASN* 3.6 12.5 + - + -
119A ASN* 5.1 0.3 + - - -
122A THR* 3.5 18.8 - - + +
124A SER* 3.2 28.4 - - - -
125A LEU* 3.4 44.0 - - + -
254A THR 3.4 13.6 + - - +
255A ILE* 3.1 19.4 + - + +
257A LYS* 1.3 79.6 - - - +
259A CYS* 1.3 65.6 + - - +
260A GLN* 4.4 4.7 - - - +
395A ILE* 3.0 40.5 - - + +
396A ASP* 2.3 33.8 + - - +
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Residues in contact with CYS 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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112A LYS* 2.2 49.2 + - + +
113A ILE* 3.0 37.0 - - + -
116A ASN* 3.9 23.6 - - - -
255A ILE* 2.8 31.2 + - - +
256A PHE 4.1 2.9 - - - +
258A TYR* 1.3 76.0 - - - +
260A GLN* 1.3 67.2 + - - +
261A LEU* 3.9 4.4 - - + +
395A ILE* 4.2 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