Contacts of the helix formed by residues 253 - 266 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B LEU* 3.6 31.2 - - - -
179B THR 3.8 7.7 + - - -
180B LEU* 2.7 29.9 + - - -
251B HIS 3.5 3.4 + - - -
252B ARG* 1.3 77.3 - - - +
254B LYS* 1.3 63.5 - - - +
255B TRP* 3.4 9.7 - - - +
256B LEU* 3.0 16.5 + - - +
257B GLU* 3.1 21.9 + - - +
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Residues in contact with LYS 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ALA* 6.0 4.9 - - - +
127B THR* 4.0 16.6 - - + +
132B GLU* 3.4 45.9 + - + +
136B LEU* 5.5 0.2 - - - +
252B ARG 3.8 0.8 + - - -
253B SER* 1.3 70.6 - - - +
255B TRP* 1.3 59.6 + - - +
257B GLU* 3.3 9.6 + - + +
258B SER* 2.7 53.9 + - - +
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Residues in contact with TRP 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ARG* 4.6 1.2 + - - -
124B MET* 3.5 31.2 - - + +
127B THR* 3.6 32.3 + - - +
128B LEU* 3.7 28.8 - - + +
136B LEU* 5.2 1.1 - - + -
180B LEU* 3.9 28.0 - - + -
181B TYR* 3.7 25.8 - + - -
253B SER* 3.4 16.8 - - - +
254B LYS* 1.3 78.5 - - - +
256B LEU* 1.3 91.7 + - + +
258B SER* 3.5 1.7 + - - -
259B TYR* 3.1 31.2 + + + +
277B LEU* 5.6 0.4 - - + -
280B GLN* 3.6 45.1 - - + -
284B THR* 4.2 13.7 - - - -
600B HEM 4.5 4.8 - - + +
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Residues in contact with LEU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LEU 3.4 16.8 - - - +
181B TYR* 3.9 32.8 - - + +
246B LEU* 4.2 17.0 - - + -
252B ARG* 3.9 29.2 - - + +
253B SER* 3.0 11.0 + - - +
255B TRP* 1.3 84.4 - - + +
257B GLU* 1.3 61.8 + - - +
259B TYR* 3.3 2.9 + - + -
260B LEU* 2.9 42.6 + - + +
277B LEU* 3.6 31.0 - - + -
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Residues in contact with GLU 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B ARG* 3.4 44.2 + - + +
253B SER 3.1 19.4 + - - +
254B LYS* 3.9 10.0 - - + +
256B LEU* 1.3 76.4 - - - +
258B SER* 1.3 58.2 + - - +
260B LEU* 3.6 9.3 - - - +
261B LEU* 3.0 27.5 + - - +
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Residues in contact with SER 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ARG* 3.0 32.0 + - - -
127B THR* 3.2 15.1 - - - +
254B LYS* 2.7 38.5 + - - +
255B TRP 3.5 1.4 + - - -
257B GLU* 1.3 74.6 - - - +
259B TYR* 1.3 60.2 + - - +
261B LEU* 3.6 8.3 - - - +
262B HIS* 2.8 29.8 + - - +
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Residues in contact with TYR 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LEU* 4.9 7.3 - - + +
120B GLU* 3.8 9.0 - - + -
123B ARG* 3.6 15.2 - - - +
124B MET* 3.5 26.0 - - + -
255B TRP* 3.1 26.4 + + + +
256B LEU* 3.7 3.8 - - + +
258B SER* 1.3 74.9 + - - +
260B LEU* 1.3 58.9 + - - +
262B HIS* 3.2 16.4 + + - +
263B LEU* 2.9 59.1 + - + +
276B ALA* 3.4 26.0 + - + +
277B LEU* 4.0 19.1 - - + -
279B LEU* 5.4 2.1 - - - +
280B GLN* 3.6 36.1 + - + -
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B PRO* 4.6 11.0 - - + -
246B LEU* 5.3 1.1 - - + -
252B ARG* 3.4 41.5 - - - +
256B LEU* 2.9 35.7 + - + +
257B GLU* 3.6 6.1 - - - +
259B TYR* 1.3 76.2 - - - +
261B LEU* 1.3 56.6 + - - +
263B LEU* 3.2 9.2 + - + +
264B GLU* 2.9 42.0 + - - +
273B GLN* 3.6 21.2 - - - +
277B LEU* 4.1 26.7 - - + -
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Residues in contact with LEU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B GLU 3.0 17.9 + - - +
258B SER* 3.6 9.6 - - - +
260B LEU* 1.3 74.5 - - - +
262B HIS* 1.3 63.5 + - - +
264B GLU* 3.5 23.9 + - + +
265B GLU* 3.0 57.4 + - + +
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Residues in contact with HIS 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LEU* 6.1 0.6 - - - +
115B TYR* 4.6 12.7 - - + -
120B GLU* 3.5 44.8 + - + +
123B ARG* 3.9 15.5 + - - +
258B SER 2.8 21.7 + - - +
259B TYR* 3.2 20.1 + + - +
261B LEU* 1.3 74.8 - - - +
263B LEU* 1.3 64.0 + - + +
265B GLU* 3.7 12.7 + - - +
266B MET* 3.3 56.5 + - + +
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Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LEU* 4.5 9.2 - - + -
259B TYR* 2.9 64.5 + - + +
260B LEU* 3.2 10.7 + - + +
262B HIS* 1.3 74.3 - - + +
264B GLU* 1.3 62.0 + - - +
266B MET* 3.0 36.2 + - + -
268B VAL* 3.2 33.3 + - + +
273B GLN* 3.9 31.2 - - + +
276B ALA* 4.2 16.6 - - + -
277B LEU* 4.9 4.3 - - + -
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Residues in contact with GLU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU* 2.9 31.7 + - - +
261B LEU* 3.5 31.1 - - + +
263B LEU* 1.3 76.2 - - - +
265B GLU* 1.3 57.2 + - + +
267B GLY* 3.2 16.6 + - - +
268B VAL 4.6 2.0 - - - +
273B GLN* 4.0 21.7 + - - +
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Residues in contact with GLU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B LEU* 3.0 52.0 + - + +
262B HIS* 3.7 12.7 + - - +
264B GLU* 1.3 76.3 - - + +
266B MET* 1.3 59.2 + - + +
267B GLY 3.3 1.2 + - - -
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Residues in contact with MET 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LEU* 4.3 14.6 - - + -
113B PRO* 3.6 36.0 - - + +
114B HIS 4.6 3.8 - - - +
115B TYR* 3.9 29.4 - - + -
262B HIS* 3.3 44.4 + - + +
263B LEU* 3.0 24.4 + - + +
265B GLU* 1.3 78.2 - - + +
267B GLY* 1.3 60.2 + - - +
268B VAL* 3.9 12.6 - - + -
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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