Contacts of the helix formed by residues 253 - 266 (chain A) in PDB entry 2IAG
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 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A LEU* 3.8 29.4 - - - -
179A THR 3.8 6.5 + - - -
180A LEU* 2.9 27.9 + - - -
251A HIS* 3.7 3.0 + - - -
252A ARG* 1.3 76.8 - - - +
254A LYS* 1.3 59.5 + - - +
255A TRP* 3.5 14.1 - - - +
256A LEU* 3.1 17.3 + - - +
257A GLU* 3.0 28.0 + - - +
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Residues in contact with LYS 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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127A THR* 3.9 17.0 - - + -
132A GLU* 3.4 41.3 + - + +
252A ARG 3.9 1.0 + - - -
253A SER* 1.3 70.2 - - - +
255A TRP* 1.3 58.9 + - - +
257A GLU* 4.4 12.0 + - + +
258A SER* 2.6 60.4 + - - +
261A LEU* 5.5 6.5 - - - +
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Residues in contact with TRP 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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123A ARG* 5.0 1.2 + - - -
124A MET* 3.4 38.1 - - + +
127A THR* 3.6 20.7 + - - +
128A LEU* 3.4 36.4 - - + +
136A LEU* 5.2 1.1 - - + -
180A LEU* 3.8 28.3 - - + -
181A TYR* 3.7 31.6 - + - -
253A SER* 3.1 16.8 - - - +
254A LYS* 1.3 77.9 - - - +
256A LEU* 1.3 94.5 + - + +
258A SER* 3.5 2.1 + - - -
259A TYR* 3.2 27.4 + + + +
277A LEU* 5.3 2.0 - - + -
280A GLN* 3.7 30.1 - - + -
284A THR* 3.8 22.9 - - + +
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Residues in contact with LEU 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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180A LEU 3.5 25.4 - - - +
181A TYR* 3.9 21.5 - - + +
246A LEU* 4.3 11.7 - - + -
252A ARG* 4.1 31.2 - - + +
253A SER* 3.1 11.7 + - - +
255A TRP* 1.3 91.4 - - + +
257A GLU* 1.3 61.1 + - + +
259A TYR* 3.0 4.0 + - + +
260A LEU* 2.8 40.6 + - + +
277A LEU* 3.5 32.1 - - + -
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Residues in contact with GLU 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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252A ARG* 3.5 55.8 + - + +
253A SER 3.0 17.1 + - - +
254A LYS* 4.2 12.0 - - + +
256A LEU* 1.3 75.3 - - - +
258A SER* 1.3 62.0 + - - +
260A LEU* 3.4 9.7 + - - +
261A LEU* 3.1 31.0 + - + +
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Residues in contact with SER 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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123A ARG* 3.0 25.8 + - - -
127A THR* 3.3 12.1 - - - +
254A LYS* 2.6 46.0 + - - +
255A TRP 3.5 2.6 + - - -
257A GLU* 1.3 74.4 - - - +
259A TYR* 1.3 60.7 + - - +
261A LEU* 3.6 12.5 + - - +
262A HIS* 3.0 27.0 + - - +
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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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112A LEU* 4.5 7.4 - - - +
120A GLU* 3.5 25.8 - - + -
123A ARG* 3.7 7.4 - - - +
124A MET* 3.5 18.4 - - + -
255A TRP* 3.2 24.9 + + + +
256A LEU* 3.0 7.6 + - + +
258A SER* 1.3 74.5 + - - +
260A LEU* 1.3 65.4 + - - +
262A HIS* 3.1 18.3 + + - +
263A LEU* 3.1 51.9 + - + +
276A ALA* 3.6 20.7 - - + +
277A LEU* 3.9 24.7 - - + -
279A LEU* 5.0 1.9 - - - +
280A GLN* 3.6 35.5 + - + -
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Residues in contact with LEU 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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243A PRO* 5.0 7.0 - - + -
246A LEU* 5.3 1.8 - - + -
252A ARG* 3.3 34.3 - - - +
256A LEU* 2.8 34.3 + - + +
257A GLU* 3.5 9.4 - - - +
259A TYR* 1.3 71.5 - - - +
261A LEU* 1.3 56.9 + - + +
263A LEU* 3.1 12.2 + - + +
264A GLU* 2.9 30.1 + - - +
273A GLN* 4.1 20.3 - - - +
277A LEU* 3.7 39.5 - - + -
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Residues in contact with LEU 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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254A LYS* 5.5 5.8 - - - +
257A GLU* 3.1 19.4 + - + +
258A SER* 3.7 14.8 - - - +
260A LEU* 1.3 78.1 - - - +
262A HIS* 1.3 58.7 + - - +
264A GLU* 3.7 29.0 - - - +
265A GLU* 2.9 30.4 + - - +
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Residues in contact with HIS 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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112A LEU* 6.0 0.8 - - - +
115A TYR* 4.6 12.3 - + + -
120A GLU* 3.7 44.7 + - + +
123A ARG* 4.0 15.3 + - - +
258A SER 3.0 14.9 + - - +
259A TYR* 3.1 23.7 + + - +
261A LEU* 1.3 74.7 - - - +
263A LEU* 1.3 63.6 + - + +
265A GLU* 3.3 20.5 + - - +
266A MET* 3.3 45.5 + - + +
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Residues in contact with LEU 263 (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 LEU* 4.4 16.6 - - + -
259A TYR* 3.1 63.9 + - + +
260A LEU* 3.4 14.1 - - + +
262A HIS* 1.3 74.0 - - + +
264A GLU* 1.3 65.3 + - - +
266A MET* 3.1 23.0 + - + -
268A VAL* 3.1 35.7 + - + +
273A GLN* 3.8 41.3 - - + +
276A ALA* 4.2 6.1 - - + -
277A LEU* 4.9 0.4 - - + -
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Residues in contact with GLU 264 (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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260A LEU 2.9 16.4 + - - +
261A LEU* 3.7 29.7 - - - +
263A LEU* 1.3 75.0 - - - +
265A GLU* 1.3 56.4 + - - +
267A GLY* 2.8 23.8 + - - +
268A VAL 4.7 8.1 - - - -
273A GLN* 4.6 8.8 - - - +
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Residues in contact with GLU 265 (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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261A LEU 2.9 14.4 + - - +
262A HIS* 3.3 16.2 + - - +
263A LEU 3.2 0.2 - - - -
264A GLU* 1.3 77.3 - - - +
266A MET* 1.3 70.6 + - - +
267A GLY 3.4 0.9 + - - -
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Residues in contact with MET 266 (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 LEU* 3.9 26.9 - - + -
113A PRO* 3.7 44.9 - - + +
114A HIS 5.0 1.3 - - - +
115A TYR* 4.0 20.4 - - + -
262A HIS* 3.3 44.6 + - + +
263A LEU* 3.1 16.7 + - + +
265A GLU* 1.3 85.3 - - - +
267A GLY* 1.3 61.2 + - - +
268A VAL* 3.3 8.7 + - + -
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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
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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