Contacts of the helix formed by residues 249 - 264 (chain E) in PDB entry 3IFS
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 ASN 249 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241E PHE* 2.9 36.7 + - - -
243E THR* 3.0 31.3 + - + +
245E GLU 3.7 7.4 - - - +
246E LEU 3.1 5.2 + - - +
247E GLU 3.5 0.6 - - - -
248E GLU* 1.3 76.2 - - - +
250E PRO* 1.3 66.5 - - - +
251E ALA* 2.9 22.9 + - - +
252E TYR* 3.0 31.3 + - + -
253E GLN* 3.0 25.9 + - - +
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Residues in contact with PRO 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MSE 6.6 0.4 - - - -
3E THR* 3.8 28.7 - - + +
5E VAL 5.3 0.4 - - - +
6E THR* 5.3 0.4 - - - -
7E PHE* 3.9 27.3 - - + +
240E ASP 4.7 0.9 - - - +
241E PHE* 3.9 21.5 - - + -
248E GLU 3.5 10.8 - - - +
249E ASN* 1.3 84.8 - - - +
251E ALA* 1.3 61.6 + - - +
253E GLN* 3.3 19.1 + - - +
254E TYR* 3.1 19.4 + - - +
400E PHE* 3.7 10.8 - - + -
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Residues in contact with ALA 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241E PHE* 3.8 21.8 - - + -
249E ASN* 2.9 12.1 + - - +
250E PRO* 1.3 80.0 - - - +
252E TYR* 1.3 66.2 + - + +
254E TYR* 3.4 0.5 + - - +
255E ALA* 3.1 17.5 + - - +
400E PHE* 3.6 34.0 - - + +
403E LYS* 4.3 4.0 - - + -
404E ALA* 3.3 24.2 - - - +
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Residues in contact with TYR 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E VAL* 3.5 21.1 - - + -
32E HIS* 2.7 33.7 + - + +
35E ILE* 4.5 1.8 - - + +
36E HIS* 4.0 0.2 + - - -
243E THR 3.2 19.5 - - - -
244E SER* 4.5 4.7 - - - -
246E LEU* 3.6 15.3 - - + -
249E ASN* 3.0 33.0 + - + +
251E ALA* 1.3 76.9 - - + +
253E GLN* 1.3 61.1 + - - +
255E ALA* 3.4 5.5 + - - +
256E VAL* 2.9 32.7 + - - +
403E LYS* 3.0 41.5 + - + -
407E MSE 3.6 39.6 - - + +
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Residues in contact with GLN 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PHE* 3.9 20.5 - - + +
9E TYR* 3.8 26.0 - - + -
21E ILE* 5.0 7.2 - - + -
246E LEU* 3.2 27.4 + - + +
247E GLU* 3.2 28.2 + - - +
248E GLU 4.5 0.4 - - - -
249E ASN 3.0 20.8 + - - +
250E PRO* 3.7 17.1 - - - +
251E ALA 3.3 0.4 - - - -
252E TYR* 1.3 77.0 - - - +
254E TYR* 1.3 57.7 + - - +
256E VAL* 3.3 3.1 + - - +
257E VAL* 2.9 34.3 + - - +
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Residues in contact with TYR 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PHE* 3.5 36.9 - + + -
250E PRO 3.1 16.1 + - - +
251E ALA 3.7 2.9 - - - +
253E GLN* 1.3 74.2 - - - +
255E ALA* 1.3 64.2 + - - +
257E VAL* 3.3 0.7 + - - +
258E ARG* 3.0 52.9 + - + +
269E GLU* 2.5 34.4 + - - -
285E TRP* 3.5 16.5 + - - -
289E PHE* 3.9 8.3 - + - -
328E THR* 3.8 19.0 + - + +
382E LEU* 4.2 5.4 - - + -
384E VAL* 5.5 0.2 - - + -
400E PHE* 4.1 13.2 - + + -
401E PHE* 3.6 27.3 - + - -
404E ALA* 3.7 20.0 - - + -
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Residues in contact with ALA 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E ALA 3.1 10.8 + - - +
252E TYR 3.7 3.6 - - - +
254E TYR* 1.3 78.0 - - - +
256E VAL* 1.3 63.6 + - - +
258E ARG* 3.5 4.9 + - - +
259E ASN* 3.2 29.8 + - - -
404E ALA 3.4 23.8 - - - +
407E MSE 3.5 20.6 - - + -
408E SER* 3.5 23.1 - - - +
411E LEU* 4.2 1.1 - - + -
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Residues in contact with VAL 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E GLU 4.2 3.1 - - - +
21E ILE* 3.9 35.0 - - + -
24E LEU* 3.7 25.3 - - + +
28E VAL* 3.5 29.6 - - + -
246E LEU* 3.8 9.0 - - + -
252E TYR 2.9 21.6 + - - +
253E GLN* 3.8 4.0 - - - +
255E ALA* 1.3 77.0 - - - +
257E VAL* 1.3 58.2 + - - +
259E ASN* 3.3 3.7 + - - +
260E ALA* 2.9 28.1 + - + +
411E LEU* 3.8 15.7 - - + -
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Residues in contact with VAL 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E PHE* 4.4 4.0 - - + -
9E TYR* 4.3 16.6 - - + -
16E ILE* 4.0 23.3 - - + -
21E ILE* 3.8 30.3 - - + -
253E GLN 2.9 26.1 + - - +
254E TYR 3.9 3.6 - - - +
256E VAL* 1.3 73.5 - - - +
258E ARG* 1.3 63.4 + - - +
260E ALA* 3.2 2.1 + - - +
261E LEU* 2.9 31.6 + - + +
382E LEU* 3.8 35.9 - - + -
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Residues in contact with ARG 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E TYR* 3.0 57.8 + - + +
255E ALA* 3.7 5.4 - - - +
257E VAL* 1.3 76.1 - - - +
259E ASN* 1.3 58.5 + - - +
261E LEU* 3.4 3.0 + - - +
262E TYR* 2.9 28.6 + - - +
269E GLU* 2.7 28.3 + - - +
285E TRP* 4.8 2.0 - - - -
289E PHE* 3.4 31.6 - - - +
293E GLU* 2.8 22.4 + - - -
300E ILE* 3.6 43.9 + - + +
302E PRO* 5.8 1.0 - - - +
326E PHE* 4.2 14.6 - - + -
382E LEU* 5.1 0.2 - - + -
404E ALA 6.5 0.2 - - - -
408E SER* 2.8 32.3 + - - +
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Residues in contact with ASN 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E LEU* 5.4 5.4 - - + -
255E ALA 3.2 18.7 + - - +
256E VAL* 3.8 5.2 - - - +
258E ARG* 1.3 77.8 - - - +
260E ALA* 1.3 64.8 + - - +
262E TYR* 3.3 11.4 + - - +
263E ASN* 3.1 31.8 + - - +
293E GLU* 5.4 0.4 - - - +
300E ILE* 6.0 1.5 - - - +
408E SER* 3.2 42.0 + - - +
411E LEU* 3.7 17.8 - - + +
412E LEU* 3.7 30.5 - - - +
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Residues in contact with ALA 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE* 3.7 22.7 - - + -
20E GLU* 3.8 23.5 - - + +
24E LEU* 5.9 3.0 - - + +
256E VAL* 2.9 15.4 + - + +
257E VAL 3.2 7.6 + - - +
259E ASN* 1.3 75.4 - - - +
261E LEU* 1.3 63.2 + - - +
263E ASN* 3.1 19.1 + - - +
264E LYS* 3.2 18.1 + - - +
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Residues in contact with LEU 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E ALA* 6.1 0.7 - - + -
15E PHE* 4.8 4.0 - - + -
16E ILE* 4.7 13.9 - - + -
257E VAL* 2.9 35.6 + - + +
258E ARG 3.7 3.6 - - - +
260E ALA* 1.3 74.3 - - - +
262E TYR* 1.3 65.0 + - - +
264E LYS* 3.0 38.0 + - + +
265E GLY 3.3 0.2 + - - -
266E LYS* 3.0 32.1 + - + +
326E PHE* 3.7 41.1 - - + -
380E PRO* 4.1 26.7 - - + -
382E LEU* 4.3 5.8 - - + -
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Residues in contact with TYR 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E ARG 2.9 18.6 + - - +
259E ASN* 3.5 10.8 - - - +
260E ALA 3.3 0.2 - - - -
261E LEU* 1.3 74.0 - - - +
263E ASN* 1.3 71.0 + - - +
265E GLY* 2.9 21.7 + - - -
266E LYS 3.4 10.6 + - - -
267E THR* 3.9 16.6 - - + +
298E LYS* 3.8 7.8 - - + +
299E GLY* 3.1 42.4 + - - -
300E ILE* 3.4 26.5 - - + -
412E LEU* 3.9 24.2 - - + -
322F ARG* 3.2 32.4 + - - +
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Residues in contact with ASN 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259E ASN* 3.1 23.1 + - - +
260E ALA* 3.1 11.5 + - - +
262E TYR* 1.3 87.0 - - - +
264E LYS* 1.3 58.7 + - + +
265E GLY 3.2 1.2 + - - -
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Residues in contact with LYS 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E PHE* 2.9 28.0 + - + +
16E ILE* 4.3 3.1 - - - +
20E GLU* 2.7 42.1 + - - +
260E ALA 3.2 10.3 + - - +
261E LEU* 3.0 32.3 + - + +
263E ASN* 1.3 75.4 - - + +
265E GLY* 1.3 59.4 + - - +
266E LYS* 4.7 15.3 + - + +
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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