Contacts of the helix formed by residues 246 - 259 (chain B) in PDB entry 4X2Q
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 246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243B PHE* 3.6 8.1 - - - -
245B GLY* 1.3 75.1 - - - +
247B THR* 1.3 64.4 + - - +
248B GLU* 4.4 5.1 - - - +
249B VAL* 3.3 27.7 + - - +
250B GLY 3.1 16.8 + - - -
269B LEU* 3.8 0.2 - - - +
270B GLY* 5.3 1.6 - - - +
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Residues in contact with THR 247 (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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262A LEU* 5.6 0.9 - - - -
245B GLY 3.8 0.4 + - - -
246B SER* 1.3 71.0 - - - +
248B GLU* 1.3 69.1 + - - +
250B GLY* 3.1 1.4 + - - -
251B LYS* 3.0 41.6 + - - +
269B LEU* 3.5 40.0 - - + +
270B GLY* 4.3 11.2 - - - +
271B GLY 5.6 0.2 - - - +
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B SER* 3.4 5.5 - - - +
247B THR* 1.3 87.6 + - - +
249B VAL* 1.3 62.4 + - + +
251B LYS* 3.7 11.9 + - + +
252B LEU* 3.6 25.7 + - + +
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B PHE* 3.8 23.3 - - + -
246B SER* 3.3 23.4 + - - +
247B THR 3.3 0.2 - - - -
248B GLU* 1.3 77.7 - - + +
250B GLY* 1.3 64.6 + - - +
252B LEU* 3.1 24.7 + - + +
253B ILE* 3.1 19.2 + - + +
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Residues in contact with GLY 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 5.7 0.2 - - - -
243B PHE* 3.6 25.9 - - - -
246B SER 3.1 12.3 + - - -
247B THR 3.1 4.6 + - - -
249B VAL* 1.3 75.1 - - - +
251B LYS* 1.3 63.0 + - - +
253B ILE* 3.2 17.2 + - - +
254B GLN* 3.4 5.5 + - - +
267B LEU* 3.6 17.0 - - - +
269B LEU* 4.0 8.5 - - - -
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Residues in contact with LYS 251 (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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258A GLY 4.0 15.8 - - - +
259A ARG* 5.6 4.6 + - - -
260A SER 4.3 15.3 + - - -
261A ASN 6.0 0.4 - - - -
262A LEU* 3.7 42.8 - - + -
247B THR* 3.0 24.6 + - - +
248B GLU* 3.8 11.4 - - + +
249B VAL 3.3 0.2 - - - -
250B GLY* 1.3 75.7 - - - +
252B LEU* 1.3 60.8 + - + +
254B GLN* 3.8 2.4 + - - +
255B GLU* 3.5 27.2 + - - +
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Residues in contact with LEU 252 (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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233B ALA* 5.4 0.3 - - - +
248B GLU 3.6 16.3 + - - +
249B VAL* 3.1 19.8 + - + +
251B LYS* 1.3 76.4 - - + +
253B ILE* 1.3 65.1 + - + +
255B GLU* 4.1 17.6 - - + +
256B ALA* 3.3 24.4 + - - +
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Residues in contact with ILE 253 (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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165B ILE* 4.3 13.5 - - + -
229B GLY 5.3 2.5 - - - +
230B ALA* 6.0 1.1 - - - -
233B ALA* 4.2 19.5 - - + +
241B ILE* 4.1 23.6 - - + -
243B PHE* 3.8 37.0 - - + -
249B VAL* 3.1 21.1 + - + +
250B GLY* 3.2 8.9 + - - +
252B LEU* 1.3 76.8 - - + +
254B GLN* 1.3 61.1 + - - +
256B ALA* 3.2 4.2 + - - +
257B ALA* 2.9 29.1 + - - +
265B VAL* 4.2 11.0 - - + -
267B LEU* 4.0 13.9 - - + -
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Residues in contact with GLN 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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254A GLN* 3.6 45.7 + - - +
255A GLU* 5.8 0.2 - - - -
257A ALA 5.4 0.2 - - - -
258A GLY* 4.9 13.6 - - - +
262A LEU* 4.5 14.0 - - + +
263A LYS 4.6 5.3 + - - -
265A VAL* 3.8 22.2 - - - +
250B GLY 3.4 10.1 + - - +
251B LYS 3.8 2.9 + - - +
253B ILE* 1.3 78.8 - - - +
255B GLU* 1.3 56.4 + - - +
257B ALA* 3.7 5.8 - - - +
258B GLY* 3.1 25.1 + - - -
265B VAL* 4.3 22.1 - - + +
267B LEU* 3.7 19.5 - - + +
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Residues in contact with GLU 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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255A GLU* 4.4 23.3 - - + +
258A GLY* 5.8 4.8 - - - -
259A ARG* 3.4 42.8 + - + +
251B LYS* 3.5 18.9 + - - +
252B LEU* 4.2 17.6 - - + +
253B ILE 3.2 0.6 - - - -
254B GLN* 1.3 80.0 - - - +
256B ALA* 1.3 61.0 + - - +
258B GLY* 3.6 1.0 + - - -
259B ARG* 3.3 52.8 + - - +
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Residues in contact with ALA 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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230B ALA* 6.5 0.9 - - + -
233B ALA* 3.4 16.1 - - + +
234B SER* 3.7 21.7 + - - +
252B LEU 3.3 16.4 + - - +
253B ILE 3.2 4.2 + - - +
255B GLU* 1.3 78.4 - - - +
257B ALA* 1.3 59.8 + - - +
259B ARG* 3.9 6.3 + - - +
260B SER* 3.1 21.1 + - - -
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Residues in contact with ALA 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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254A GLN* 5.6 0.7 - - - +
233B ALA 3.5 7.6 + - - +
241B ILE* 4.8 3.1 - - + -
253B ILE* 2.9 16.8 + - + +
254B GLN 3.7 4.7 - - - +
256B ALA* 1.3 77.3 - - - +
258B GLY* 1.3 62.2 + - - +
259B ARG 3.3 0.4 - - - -
260B SER* 2.8 19.7 + - - -
261B ASN* 3.9 1.4 - - - +
262B LEU* 3.2 18.7 + - - -
263B LYS* 3.8 24.5 - - + +
265B VAL* 3.9 18.8 - - + -
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Residues in contact with GLY 258 (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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251A LYS* 3.9 23.1 - - - +
254A GLN* 3.8 24.6 + - - -
255A GLU* 6.0 3.8 - - - -
254B GLN 3.1 14.5 + - - -
255B GLU 3.6 2.6 + - - -
257B ALA* 1.3 76.3 - - - +
259B ARG* 1.3 59.8 + - - +
260B SER 3.2 2.9 + - - -
262B LEU* 3.7 21.8 - - - +
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Residues in contact with ARG 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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251A LYS* 5.1 6.5 + - + +
255A GLU* 3.9 28.0 + - + +
259A ARG* 4.0 13.1 - - - +
255B GLU* 3.3 44.9 + - - +
256B ALA* 3.9 6.9 + - - +
257B ALA 3.3 0.8 - - - -
258B GLY* 1.3 76.3 - - - +
260B SER* 1.3 59.3 + - - +
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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
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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