Contacts of the helix formed by residues 249 - 264 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C ASP 4.8 0.2 - - - -
241C PHE* 3.0 36.2 + - - +
243C THR* 2.9 25.6 + - + +
245C GLU 3.1 12.5 + - - +
246C LEU 3.1 7.0 + - - +
247C GLU 3.6 0.4 - - - -
248C GLU* 1.3 79.6 - - - +
250C PRO* 1.3 64.1 - - - +
251C ALA* 3.1 22.3 + - - +
252C TYR* 3.1 32.0 + - + -
253C GLN* 3.0 24.5 + - - +
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Residues in contact with PRO 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL 5.7 4.0 - - - +
6C THR* 5.5 2.5 - - - -
7C PHE* 3.8 26.7 - - + +
240C ASP* 4.9 1.8 - - + +
241C PHE* 3.8 25.6 - - + -
248C GLU 3.4 11.2 - - - +
249C ASN* 1.3 83.8 - - - +
251C ALA* 1.3 59.4 + - - +
253C GLN* 3.3 18.3 + - - +
254C TYR* 3.1 23.4 + - - +
400C PHE* 3.7 7.8 - - + -
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Residues in contact with ALA 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C PHE* 3.9 22.3 - - + -
249C ASN* 3.1 10.1 + - - +
250C PRO* 1.3 79.2 - - - +
252C TYR* 1.3 65.3 + - + +
254C TYR* 3.4 1.9 + - - +
255C ALA 3.2 16.6 + - - -
400C PHE* 3.7 34.8 - - + +
403C LYS* 4.3 4.7 - - + -
404C ALA* 3.3 23.3 - - - +
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Residues in contact with TYR 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C VAL* 3.5 20.9 - - + -
32C HIS* 2.6 33.3 + - + +
35C ILE* 4.6 4.6 - - + +
36C HIS* 4.3 0.2 + - - -
243C THR 3.4 11.7 - - - -
244C SER* 4.6 2.7 - - - -
246C LEU* 3.7 15.9 - - + -
249C ASN* 3.1 41.8 + - + +
251C ALA* 1.3 79.3 - - + +
253C GLN* 1.3 59.8 + - - +
255C ALA* 3.3 5.1 + - - +
256C VAL* 2.9 33.1 + - - +
403C LYS* 2.7 42.5 + - + +
407C MSE 3.6 40.8 - - + +
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Residues in contact with GLN 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE* 3.8 20.2 - - + +
9C TYR* 3.9 24.8 - - + +
21C ILE* 4.8 8.5 - - + -
246C LEU* 3.0 30.8 + - + +
247C GLU* 3.0 31.9 + - - +
248C GLU 4.4 0.6 - - - -
249C ASN 3.0 16.8 + - - +
250C PRO* 3.7 17.7 - - - +
251C ALA 3.3 0.2 - - - -
252C TYR* 1.3 73.7 - - - +
254C TYR* 1.3 64.9 + - - +
256C VAL* 3.3 2.3 + - - +
257C VAL* 2.9 29.9 + - - +
437F GLY* 5.6 0.4 - - - -
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Residues in contact with TYR 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PHE* 3.5 34.4 - + + -
250C PRO 3.1 16.9 + - - +
251C ALA 3.7 3.1 - - - +
253C GLN* 1.3 77.1 - - - +
255C ALA* 1.3 55.4 + - - +
257C VAL* 3.8 0.7 - - - +
258C ARG* 2.9 56.8 + - + +
269C GLU* 2.6 32.5 + - - -
285C TRP* 3.5 18.4 + - - -
289C PHE* 3.8 12.3 - + - -
328C THR* 3.8 17.9 - - + +
382C LEU* 4.3 6.1 - - + -
384C VAL* 5.6 0.2 - - + -
400C PHE* 4.1 16.6 - + + -
401C PHE* 3.7 22.6 - + - -
404C ALA* 3.7 19.7 - - + -
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Residues in contact with ALA 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C ALA 3.2 10.9 + - - +
252C TYR 3.6 7.2 - - - +
253C GLN 3.3 0.4 - - - -
254C TYR* 1.3 80.0 - - - +
256C VAL* 1.3 61.7 + - - +
258C ARG* 3.6 5.8 + - - +
259C ASN* 3.1 31.4 + - - -
404C ALA 3.5 25.1 - - - +
407C MSE 3.7 14.6 - - + -
408C SER* 3.6 22.2 - - - +
411C LEU* 4.4 2.0 - - + -
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Residues in contact with VAL 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLU 4.1 4.3 - - - +
21C ILE* 3.9 34.3 - - + -
24C LEU* 3.9 23.9 - - + +
28C VAL* 3.6 30.1 - - + -
246C LEU* 3.7 11.7 - - + -
252C TYR* 2.9 20.9 + - + +
253C GLN* 3.8 4.0 - - - +
255C ALA* 1.3 72.3 - - - +
257C VAL* 1.3 61.6 + - - +
259C ASN* 3.3 3.6 + - - +
260C ALA* 2.9 29.2 + - + +
411C LEU* 3.8 14.1 - - + -
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Residues in contact with VAL 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE* 4.5 1.8 - - + -
9C TYR* 4.2 17.3 - - + -
16C ILE* 4.1 22.4 - - + -
21C ILE* 3.7 28.5 - - + -
253C GLN 2.9 22.1 + - - +
254C TYR* 3.8 5.2 - - - +
256C VAL* 1.3 76.1 - - - +
258C ARG* 1.3 64.0 + - - +
260C ALA* 3.2 2.1 + - - +
261C LEU* 2.9 31.8 + - + +
382C LEU* 3.7 35.9 - - + -
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Residues in contact with ARG 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C TYR* 2.9 63.6 + - + +
255C ALA* 3.7 6.5 - - - +
256C VAL 3.3 0.2 - - - -
257C VAL* 1.3 77.5 - - - +
259C ASN* 1.3 59.2 + - - +
261C LEU* 3.4 2.8 + - - +
262C TYR* 3.0 28.1 + - - +
269C GLU* 2.8 29.1 + - - +
285C TRP* 4.8 2.0 - - - -
289C PHE* 3.5 30.1 - - - +
293C GLU* 2.9 24.0 + - - -
300C ILE* 3.5 43.9 + - + +
302C PRO* 5.9 0.6 - - - +
326C PHE* 4.2 13.9 - - + -
382C LEU* 5.3 0.2 - - + -
408C SER* 2.8 32.1 + - - -
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Residues in contact with ASN 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LEU* 5.7 4.0 - - + -
255C ALA 3.1 23.7 + - - +
256C VAL* 3.8 4.5 - - - +
257C VAL 3.2 0.2 - - - -
258C ARG* 1.3 81.5 - - - +
260C ALA* 1.3 64.2 + - - +
262C TYR* 3.5 8.9 + - - +
263C ASN* 3.2 32.0 + - - +
293C GLU* 4.6 0.6 + - - -
300C ILE* 5.3 1.7 - - - +
408C SER* 3.2 34.7 + - - +
411C LEU* 4.1 14.5 - - + +
412C LEU* 3.6 33.0 - - - +
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Residues in contact with ALA 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B LYS* 3.7 12.7 - - - +
16C ILE* 3.6 27.1 - - + -
20C GLU* 3.9 20.6 - - + +
24C LEU* 6.5 0.2 - - + -
256C VAL* 2.9 18.2 + - + +
257C VAL 3.2 0.9 + - - +
259C ASN* 1.3 74.9 - - - +
261C LEU* 1.3 64.8 + - - +
263C ASN* 3.1 16.6 + - - +
264C LYS* 3.2 18.5 + - - +
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Residues in contact with LEU 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ALA* 5.9 0.7 - - + -
15C PHE* 4.8 3.6 - - + -
16C ILE* 4.7 13.2 - - + -
257C VAL* 2.9 37.8 + - + +
258C ARG 3.7 4.3 - - - +
260C ALA* 1.3 77.9 - - - +
262C TYR* 1.3 61.4 + - - +
264C LYS* 3.0 36.1 + - + +
265C GLY 3.3 0.2 + - - -
266C LYS* 3.0 32.6 + - + +
326C PHE* 3.7 38.6 - - + -
380C PRO* 4.0 28.5 - - + -
382C LEU* 4.3 5.6 - - + -
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Residues in contact with TYR 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ARG* 4.7 2.4 + - - -
262B TYR* 5.5 0.3 - - - -
263B ASN* 2.6 52.0 + - - -
258C ARG 3.0 17.0 + - - +
259C ASN* 3.6 11.2 - - - +
260C ALA 3.3 0.2 - - - -
261C LEU* 1.3 75.3 - - - +
263C ASN* 1.3 61.9 - - - +
265C GLY* 3.0 18.7 + - - -
266C LYS 3.5 10.8 + - - -
267C THR* 4.0 17.1 - - + +
299C GLY* 3.0 41.4 + - - -
300C ILE* 3.4 26.0 - - + -
412C LEU* 3.8 17.9 - - + -
322D ARG* 3.2 24.4 + - - +
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Residues in contact with ASN 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ARG* 3.7 2.1 - - - -
262B TYR* 2.6 44.2 + - + -
263B ASN* 3.4 22.0 - - - +
298B LYS* 3.6 24.3 - - + +
411B LEU 5.5 0.8 + - - -
412B LEU* 3.7 28.2 + - + +
259C ASN* 3.2 20.9 + - - +
260C ALA* 3.1 11.6 + - - +
262C TYR* 1.3 78.2 - - - +
264C LYS* 1.3 56.9 + - - +
265C GLY 3.2 1.9 + - - -
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Residues in contact with LYS 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ARG* 3.7 13.0 + - - -
323A ARG 5.6 1.2 + - - -
296B ASP 2.7 36.2 + - - +
297B GLN* 3.3 25.6 + - + +
298B LYS* 3.9 5.2 - - + +
15C PHE* 2.9 27.5 + - + +
16C ILE* 4.3 7.9 - - - +
20C GLU* 2.8 38.2 + - - -
260C ALA 3.2 12.5 + - - +
261C LEU* 3.0 24.0 + - + +
263C ASN* 1.3 75.0 - - - +
265C GLY* 1.3 59.5 + - - +
266C LYS* 3.9 15.1 + - + -
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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
------------------------------------------------------------
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