Contacts of the helix formed by residues 257 - 272 (chain B) in PDB entry 2QLF
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 GLU 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256B LEU* 1.3 71.5 - - - +
258B ILE* 1.3 87.9 + - - +
259B MET* 2.7 37.2 + - - +
260B GLN* 2.7 42.3 + - + +
261B ILE 3.1 9.0 + - - -
295B LEU* 5.1 0.3 - - - +
297B LYS 4.4 2.4 - - - +
298B GLU* 3.7 26.6 - - + +
299B LEU 3.0 32.0 + - - +
300B TYR* 3.1 21.9 - - + +
812G HIS* 4.4 9.4 - - + -
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Residues in contact with ILE 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 4.9 3.1 - - + -
182A PHE* 4.6 13.7 - - + -
220B LEU* 4.0 19.1 - - + -
249B LEU* 5.7 1.3 - - + -
256B LEU 3.6 1.2 + - - -
257B GLU* 1.3 96.0 - - - +
259B MET* 1.3 64.2 + - + +
261B ILE* 3.3 16.9 + - + +
262B LEU* 2.9 44.6 + - + +
295B LEU* 4.1 15.9 - - + -
299B LEU* 2.7 38.2 + - + +
301B PHE* 4.0 26.0 - - + -
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Residues in contact with MET 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 4.1 17.3 - - - -
257B GLU* 2.7 29.3 + - - +
258B ILE* 1.3 75.0 - - + +
260B GLN* 1.3 55.5 + - + +
262B LEU* 3.8 2.2 - - + +
263B THR* 2.6 43.3 + - - +
291B VAL* 3.6 39.5 - - + -
293B SER* 4.3 7.9 - - - +
295B LEU* 5.9 1.3 - - + -
559D MET* 3.8 57.0 - - + -
563D THR* 5.1 6.3 - - - +
593D SER* 4.5 5.8 - - - -
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Residues in contact with GLN 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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256B LEU* 3.5 32.0 - - + +
257B GLU* 2.7 36.9 + - + +
259B MET* 1.3 70.2 - - + +
261B ILE* 1.3 67.7 + - - +
263B THR* 3.1 5.0 + - - -
264B ARG* 2.9 32.9 + - - +
300B TYR* 4.3 2.3 + - - -
557D GLU* 6.6 0.2 - - - -
598D GLU* 2.9 33.0 + - + +
812G HIS* 2.9 49.1 + - + +
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Residues in contact with ILE 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 4.6 0.7 - - + -
248B ILE* 3.8 20.9 - - + +
249B LEU* 3.8 27.6 - - + +
252B HIS 4.1 4.5 - - - +
253B GLY* 3.9 26.5 - - - +
256B LEU* 3.3 35.2 - - + +
257B GLU 3.1 8.0 + - - +
258B ILE* 3.3 20.4 - - + +
260B GLN* 1.3 78.7 - - - +
262B LEU* 1.3 66.2 + - + +
264B ARG* 3.1 4.3 + - - +
265B VAL* 3.0 35.5 + - + +
301B PHE* 4.6 5.6 - - + -
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PHE* 4.2 12.1 - - + -
220B LEU* 3.9 19.3 - - + -
222B ALA* 3.7 26.9 - - + -
241B PHE* 5.1 5.6 - - + -
245B LEU* 4.0 27.4 - - + -
258B ILE* 2.9 38.1 + - + +
259B MET* 4.2 4.5 - - + +
261B ILE* 1.3 75.5 - - + +
263B THR* 1.3 58.2 + - - +
265B VAL* 3.6 9.6 - - + +
266B ASN* 3.0 30.5 + - - +
291B VAL* 3.7 26.1 - - + +
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Residues in contact with THR 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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259B MET* 2.6 33.8 + - - +
260B GLN* 3.6 6.5 - - - -
262B LEU* 1.3 73.8 - - - +
264B ARG* 1.3 67.4 + - + +
265B VAL 3.1 0.2 - - - -
266B ASN* 3.3 8.3 + - - +
267B ASP* 3.2 20.4 + - - +
291B VAL* 5.9 0.4 - - - +
559D MET* 5.1 5.4 - - - +
593D SER* 4.8 6.1 + - - -
595D LEU* 3.7 11.1 + - + +
596D THR* 3.7 2.3 - - - -
597D LYS* 3.3 44.4 - - - +
598D GLU* 4.5 4.7 - - + +
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Residues in contact with ARG 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ILE* 4.2 25.7 - - + +
252B HIS* 3.2 33.3 + - - -
256B LEU* 3.5 35.6 - - - +
260B GLN* 2.9 18.1 + - - +
261B ILE 3.5 7.4 - - - +
263B THR* 1.3 78.7 - - + +
265B VAL* 1.3 58.3 + - - +
267B ASP* 3.5 6.8 + - - +
268B ARG* 3.1 27.4 + - - +
358C TYR* 3.5 64.6 + - + +
596D THR 5.6 0.4 - - - -
598D GLU* 5.0 9.2 + - - +
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Residues in contact with VAL 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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241B PHE* 3.9 28.7 - - + -
244B ALA* 3.8 7.0 - - + -
245B LEU* 3.6 43.1 - - + +
248B ILE* 3.9 23.6 - - + -
261B ILE 3.0 20.8 + - - +
262B LEU* 3.6 12.8 - - + +
263B THR 3.1 0.2 - - - -
264B ARG* 1.3 76.1 - - - +
266B ASN* 1.3 64.0 + - - +
268B ARG* 3.3 3.6 + - - +
269B VAL* 3.0 23.6 + - + +
289B PRO* 4.9 0.4 - - + -
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Residues in contact with ASN 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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262B LEU 3.0 18.3 + - - +
263B THR* 3.3 7.7 + - - +
265B VAL* 1.3 78.4 - - - +
267B ASP* 1.3 57.3 + - - +
269B VAL 3.4 0.2 + - - -
270B ALA* 3.0 30.1 + - - +
288B ILE* 3.6 13.4 - - + +
289B PRO* 2.8 41.0 - - - +
290B CYS 4.2 0.3 + - - -
291B VAL* 4.2 10.1 - - - +
593D SER* 3.6 24.7 + - - -
594D MET* 3.9 4.6 - - - +
595D LEU 3.0 28.5 + - - +
596D THR* 4.2 0.4 - - + -
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Residues in contact with ASP 267 (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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263B THR 3.2 5.5 + - - +
264B ARG* 3.8 8.7 - - - +
265B VAL 3.3 0.2 - - - -
266B ASN* 1.3 79.5 - - - +
268B ARG* 1.3 59.5 + - - +
270B ALA* 4.3 0.7 - - - -
271B ARG* 2.9 61.4 + - - +
596D THR* 3.3 31.2 - - - +
597D LYS* 3.0 30.2 + - - -
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Residues in contact with ARG 268 (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 GLN* 6.0 0.6 - - - +
244B ALA* 3.9 20.9 - - + +
247B SER* 4.8 18.0 + - - +
248B ILE* 5.1 10.0 - - + +
264B ARG 3.1 18.2 + - - +
265B VAL* 3.3 5.8 + - - +
267B ASP* 1.3 77.8 + - - +
269B VAL* 1.3 57.9 + - - +
271B ARG* 4.6 0.7 - - - +
272B HIS* 2.8 83.0 + - - +
273B PHE* 3.3 23.4 - - - -
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Residues in contact with VAL 269 (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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240B TRP* 3.8 13.3 - - + +
241B PHE* 3.8 19.5 - - - -
244B ALA* 3.6 21.3 - - + -
265B VAL* 3.0 21.1 + - + +
268B ARG* 1.3 76.3 - - - +
270B ALA* 1.3 62.4 + - - +
271B ARG 3.5 0.2 - - - -
273B PHE* 3.8 22.4 - - - +
286B LYS* 4.7 0.2 + - - -
287B GLN* 3.0 45.3 + - + +
289B PRO* 3.6 24.7 - - + -
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Residues in contact with ALA 270 (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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266B ASN 3.0 16.9 + - - +
267B ASP* 3.8 6.1 - - - +
269B VAL* 1.3 80.8 - - - +
271B ARG* 1.3 59.7 + - + +
286B LYS* 2.7 31.6 + - - -
287B GLN 3.5 6.9 + - - -
288B ILE* 3.8 13.9 - - + -
512D LYS 3.7 3.1 - - - +
513D ILE* 4.6 0.6 - - + -
514D PRO* 3.7 27.2 - - + +
517D ALA* 4.9 0.4 - - + -
596D THR* 4.3 6.5 - - + -
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Residues in contact with ARG 271 (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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267B ASP* 2.9 39.9 + - - +
268B ARG* 5.3 0.2 - - - -
270B ALA* 1.3 86.0 - - + +
272B HIS* 1.3 57.5 + - + +
273B PHE 3.3 8.1 + - - +
286B LYS* 4.1 5.7 + - - +
360C TYR* 6.1 1.2 - - - -
476C GLU* 2.8 38.7 + - - +
511D TYR 5.2 7.6 + - - -
512D LYS 4.8 4.1 - - - +
513D ILE* 4.7 19.3 - - + +
518D ASP* 6.0 0.2 + - - -
596D THR* 4.5 8.5 + - - +
597D LYS* 3.6 21.1 - - - +
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Residues in contact with HIS 272 (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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237B ARG* 6.1 3.1 - - - -
268B ARG* 2.8 65.1 + - - +
271B ARG* 1.3 77.4 - - + +
273B PHE* 1.3 76.1 + + - +
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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