Contacts of the helix formed by residues 251 - 271 (chain A) in PDB entry 4FLL
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 ASP 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A GLY* 5.1 1.8 + - - -
250A VAL* 1.3 78.8 - - - +
252A ASP* 1.3 65.6 + - - +
253A GLY 3.2 4.3 + - - -
254A ALA* 2.9 31.6 + - - +
255A ARG* 3.1 21.7 + - - +
362A ARG* 3.0 28.8 + - - -
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Residues in contact with ASP 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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251A ASP* 1.3 76.1 - - - +
253A GLY* 1.3 58.5 + - - +
255A ARG* 2.9 26.9 + - - +
256A LYS* 3.0 29.6 + - - +
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Residues in contact with GLY 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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251A ASP* 3.2 7.8 + - - -
252A ASP* 1.3 76.4 - - - +
254A ALA* 1.3 60.3 + - - +
256A LYS* 3.4 7.2 + - - +
257A LEU* 2.9 30.5 + - - +
294A PHE* 4.7 3.1 - - - -
341A GLU* 4.2 7.9 - - - +
362A ARG* 3.8 9.9 - - - -
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Residues in contact with ALA 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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223A GLY 5.0 0.2 - - - +
225A ILE* 3.7 24.5 - - + -
246A PHE* 4.4 1.6 - - - -
250A VAL* 3.8 16.4 - - + -
251A ASP* 2.9 22.3 + - - +
253A GLY* 1.3 76.3 - - - +
255A ARG* 1.3 62.4 + - - +
257A LEU* 3.8 5.3 - - - +
258A VAL* 3.0 30.7 + - - +
362A ARG* 3.4 20.7 - - - +
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Residues in contact with ARG 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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246A PHE* 4.0 21.2 - - + -
249A GLU* 4.3 14.3 + - - +
250A VAL* 2.5 51.2 + - + +
251A ASP* 3.1 13.1 + - - +
252A ASP* 2.9 37.2 + - - +
254A ALA* 1.3 76.1 - - - +
256A LYS* 1.3 57.2 + - - +
258A VAL* 4.0 0.9 - - - +
259A GLN* 3.0 31.6 + - - +
391A PHE* 5.3 0.5 - - - -
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Residues in contact with LYS 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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252A ASP 3.0 17.3 + - - +
253A GLY* 3.8 6.3 - - - +
255A ARG* 1.3 73.4 - - - +
257A LEU* 1.3 62.1 + - - +
259A GLN* 3.9 4.0 - - - +
260A THR* 2.7 39.1 + - - +
292A ASN* 2.8 48.5 + - - +
294A PHE* 3.8 15.3 - - + -
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Residues in contact with LEU 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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225A ILE* 4.0 11.2 - - + -
253A GLY 2.9 18.6 + - - +
254A ALA* 3.3 4.5 + - - +
256A LYS* 1.3 77.0 - - - +
258A VAL* 1.3 59.6 + - - +
260A THR* 3.8 1.2 - - - -
261A THR* 2.8 34.6 + - - +
294A PHE* 3.6 20.2 - - + -
339A ILE* 3.6 37.5 - - + +
340A CYS 4.1 0.9 - - - -
341A GLU* 3.9 17.9 - - + +
362A ARG* 3.7 40.6 - - + +
363A SER 3.9 1.3 - - - +
364A ALA* 3.9 15.7 - - + +
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Residues in contact with VAL 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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225A ILE* 4.2 12.1 - - + -
244A THR* 3.8 28.5 - - + +
246A PHE* 3.8 20.2 - - + -
254A ALA 3.0 16.8 + - - +
257A LEU* 1.3 79.4 - - + +
259A GLN* 1.3 65.7 + - - +
261A THR 3.2 1.4 + - - -
262A TYR* 3.0 22.0 + - - +
364A ALA* 4.0 13.5 - - + -
366A PHE* 3.6 27.3 - - + -
391A PHE* 3.7 24.0 - - + -
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Residues in contact with GLN 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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255A ARG 3.0 20.3 + - - +
256A LYS* 3.9 4.7 - - - +
258A VAL* 1.3 76.4 - - - +
260A THR* 1.3 65.8 + - - +
262A TYR* 3.2 6.3 + - - +
263A GLU* 3.0 61.6 + - - +
391A PHE* 3.3 22.5 - - + -
392A MET* 2.9 38.1 - - - +
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Residues in contact with THR 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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256A LYS* 2.7 30.0 + - - +
257A LEU 3.8 1.1 - - - -
259A GLN* 1.3 73.6 - - - +
261A THR* 1.3 58.6 + - - +
263A GLU* 3.3 12.6 + - - +
264A CYS* 2.9 33.3 + - - -
288A HIS* 3.8 13.5 - - + +
289A ALA* 4.3 2.5 - - - -
292A ASN* 3.7 33.1 + - + +
294A PHE* 3.5 31.4 - - + -
339A ILE* 5.1 2.0 - - + -
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Residues in contact with THR 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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257A LEU* 2.8 22.6 + - - +
258A VAL 3.6 4.7 - - - -
260A THR* 1.3 75.0 - - - +
262A TYR* 1.3 64.5 + - - +
264A CYS* 3.2 5.3 + - - +
265A LEU* 3.1 21.5 + - - +
337A PRO* 3.6 11.6 - - + +
339A ILE* 3.3 32.0 - - + +
364A ALA* 3.3 34.4 - - - +
365A GLN* 3.6 21.8 - - - +
366A PHE* 3.9 5.6 - - + +
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Residues in contact with TYR 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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258A VAL 3.0 16.7 + - - +
259A GLN* 3.2 11.4 + - - +
261A THR* 1.3 75.1 - - - +
263A GLU* 1.3 66.7 + - + +
265A LEU* 3.2 5.9 + - + +
266A MET* 3.0 58.9 + - + +
366A PHE* 3.6 37.2 - + + -
368A HIS* 5.1 9.5 + - - -
389A PRO* 3.5 39.8 - - + +
391A PHE* 3.8 15.3 - + + -
392A MET* 4.7 9.0 - - + -
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Residues in contact with GLU 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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259A GLN* 3.0 47.4 + - - +
260A THR* 3.5 13.0 + - - +
262A TYR* 1.3 81.2 - - + +
264A CYS* 1.3 56.7 + - - +
266A MET* 3.8 5.3 - - - +
267A GLN* 2.9 41.1 + - + +
288A HIS* 2.7 40.0 + - + +
292A ASN* 4.9 1.2 + - - -
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Residues in contact with CYS 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 THR* 2.9 24.6 + - - -
261A THR* 3.4 10.1 - - - +
263A GLU* 1.3 76.1 - - - +
265A LEU* 1.3 63.5 + - - +
267A GLN* 3.5 4.0 + - - +
268A ALA* 3.1 23.0 + - - +
284A ILE 5.8 0.2 - - - -
285A ILE* 3.6 45.7 - - + +
288A HIS* 3.8 12.1 - - - -
289A ALA* 3.8 23.8 - - - -
337A PRO* 4.5 4.7 - - + -
339A ILE* 4.3 10.1 - - + -
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Residues in contact with LEU 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 THR 3.1 9.6 + - - +
262A TYR* 3.2 10.1 + - + +
264A CYS* 1.3 79.6 - - - +
266A MET* 1.3 66.2 + - - +
268A ALA* 3.2 5.0 + - - +
269A ILE* 3.0 35.4 + - + +
335A ILE* 3.4 43.7 - - + +
337A PRO* 3.9 14.3 - - + +
366A PHE* 3.5 35.9 - - + -
367A GLU* 3.8 3.6 - - - +
368A HIS* 3.8 25.4 - - + +
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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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262A TYR* 3.0 56.4 + - + +
263A GLU* 4.0 5.4 - - - +
265A LEU* 1.3 74.9 - - - +
267A GLN* 1.3 62.6 + - + +
269A ILE* 3.3 23.3 + - + +
270A ASP* 2.9 45.3 + - - +
368A HIS* 4.3 11.2 - - - +
379A ILE* 4.0 25.1 - - + -
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Residues in contact with GLN 267 (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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263A GLU* 2.9 24.3 + - + +
264A CYS* 4.0 2.5 - - - +
266A MET* 1.3 77.0 - - + +
268A ALA* 1.3 64.0 + - - +
270A ASP* 3.3 19.5 + - - +
271A ALA* 3.3 11.1 + - - +
284A ILE* 3.8 24.7 - - + +
288A HIS* 3.4 48.7 + - - +
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Residues in contact with ALA 268 (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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264A CYS 3.1 15.1 + - - +
265A LEU 3.5 7.6 - - - +
267A GLN* 1.3 73.9 - - - +
269A ILE* 1.3 65.5 + - - +
271A ALA* 3.1 9.9 + - - +
272A VAL* 3.5 3.6 + - - +
281A LEU* 3.4 30.7 - - + +
284A ILE* 3.9 8.9 - - - +
285A ILE* 3.9 25.4 - - + -
335A ILE* 4.1 18.6 - - + -
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Residues in contact with ILE 269 (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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265A LEU* 3.0 26.7 + - + +
266A MET* 3.7 27.1 - - + +
268A ALA* 1.3 75.9 - - - +
270A ASP* 1.3 65.6 + - - +
272A VAL* 3.0 25.5 + - - +
335A ILE* 4.2 1.3 - - + -
368A HIS* 3.7 31.6 - - + -
370A LEU* 3.7 26.0 - - + -
377A CYS* 3.7 24.4 - - - -
379A ILE* 3.9 19.3 - - + -
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Residues in contact with ASP 270 (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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266A MET* 2.9 34.1 + - - +
267A GLN* 3.5 12.0 - - - +
268A ALA 3.2 0.4 - - - -
269A ILE* 1.3 80.9 - - - +
271A ALA* 1.3 58.5 + - - +
272A VAL 3.4 2.6 - - - +
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Residues in contact with ALA 271 (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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267A GLN 3.3 3.9 + - - +
268A ALA 3.1 8.0 + - - +
269A ILE 3.0 0.8 - - - -
270A ASP* 1.3 79.6 - - - +
272A VAL* 1.4 61.4 + - - +
273A LYS* 3.4 7.7 + - - +
276A VAL* 3.6 23.8 - - + +
280A GLU* 5.8 0.7 - - + -
281A LEU* 4.2 6.1 - - + -
284A ILE* 3.2 35.0 - - + -
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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