Contacts of the helix formed by residues 249 - 264 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A ASP 5.0 0.2 - - - -
241A PHE* 2.9 39.8 + - - +
243A THR* 3.0 23.9 + - + +
245A GLU 3.2 12.3 + - - +
246A LEU 3.1 6.2 + - - +
247A GLU 3.5 0.6 - - - -
248A GLU* 1.3 78.3 - - - +
250A PRO* 1.3 64.0 - - - +
251A ALA* 3.1 22.5 + - - +
252A TYR* 3.1 31.0 + - + -
253A GLN* 3.0 26.0 + - - +
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Residues in contact with PRO 250 (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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3A THR* 3.9 27.8 - - + +
5A VAL 5.1 1.6 - - - +
6A THR* 5.4 0.2 - - - -
7A PHE* 3.8 26.7 - - + +
240A ASP 5.2 0.2 - - - +
241A PHE* 3.8 22.7 - - + -
248A GLU 3.4 11.2 - - - +
249A ASN* 1.3 85.5 - - - +
251A ALA* 1.3 60.7 + - - +
253A GLN* 3.3 18.8 + - - +
254A TYR* 3.1 22.7 + - - +
400A PHE* 3.8 7.8 - - + -
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Residues in contact with ALA 251 (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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241A PHE* 3.9 20.7 - - + -
249A ASN* 3.1 11.3 + - - +
250A PRO* 1.3 79.3 - - - +
252A TYR* 1.3 66.1 + - + +
254A TYR* 3.4 1.6 + - - +
255A ALA 3.2 15.9 + - - -
400A PHE* 3.6 35.3 - - + +
403A LYS* 4.4 4.7 - - + -
404A ALA* 3.4 25.2 - - - +
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Residues in contact with TYR 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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28A VAL* 3.4 22.7 - - + -
32A HIS* 2.7 33.5 + - + +
35A ILE* 4.4 4.3 - - + +
36A HIS* 4.2 0.2 + - - -
243A THR 3.4 12.6 - - - -
244A SER* 4.7 2.7 - - - -
246A LEU* 3.6 15.7 - - + -
249A ASN* 3.1 40.4 + - + +
251A ALA* 1.3 77.6 - - + +
253A GLN* 1.3 60.9 + - - +
255A ALA* 3.3 5.7 + - - +
256A VAL* 2.9 33.3 + - - +
403A LYS* 2.7 40.2 + - + +
407A MSE 3.5 39.3 - - + +
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Residues in contact with GLN 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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7A PHE* 3.8 19.2 - - + +
9A TYR* 3.9 25.2 - - + -
21A ILE* 4.9 8.1 - - + -
246A LEU* 3.0 34.5 + - + +
247A GLU* 3.2 24.2 + - - +
248A GLU 4.4 0.8 - - - -
249A ASN 3.0 20.7 + - - +
250A PRO* 3.5 18.4 - - - +
252A TYR* 1.3 77.9 - - - +
254A TYR* 1.3 56.5 + - - +
256A VAL* 3.4 2.8 + - - +
257A VAL* 2.9 34.7 + - - +
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Residues in contact with TYR 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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7A PHE* 3.6 34.0 - + + -
250A PRO 3.1 13.6 + - - +
251A ALA 3.6 6.5 - - - +
252A TYR 3.3 0.2 - - - -
253A GLN* 1.3 77.4 - - - +
255A ALA* 1.3 55.9 + - - +
257A VAL* 3.4 0.5 + - - +
258A ARG* 2.9 46.8 + - + +
269A GLU* 2.6 31.9 + - - -
285A TRP* 3.3 18.9 + - - -
289A PHE* 3.9 13.0 - + - -
328A THR* 3.8 18.8 + - + +
382A LEU* 4.3 7.9 - - + -
384A VAL* 5.4 0.7 - - + -
400A PHE* 4.1 16.4 - + + -
401A PHE* 3.5 27.1 - + - -
404A ALA* 3.7 19.5 - - + -
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Residues in contact with ALA 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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251A ALA 3.2 7.7 + - - +
252A TYR 3.5 8.1 - - - +
253A GLN 3.3 0.2 - - - -
254A TYR* 1.3 80.4 - - - +
256A VAL* 1.3 61.6 + - - +
258A ARG* 3.4 9.6 - - - +
259A ASN* 3.0 32.0 + - - -
404A ALA 3.5 23.8 - - - +
407A MSE 3.6 16.6 - - + -
408A SER* 3.6 18.4 - - - +
411A LEU* 4.4 1.3 - - + -
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Residues in contact with VAL 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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20A GLU 4.2 4.7 - - - +
21A ILE* 3.9 34.5 - - + -
24A LEU* 4.0 20.9 - - + -
28A VAL* 3.6 28.9 - - + -
246A LEU* 3.9 9.0 - - + -
252A TYR 2.9 20.7 + - - +
253A GLN* 3.8 4.3 - - - +
255A ALA* 1.3 75.2 - - - +
257A VAL* 1.3 59.0 + - - +
259A ASN* 3.3 3.9 + - - +
260A ALA* 2.9 29.5 + - + +
411A LEU* 3.8 14.6 - - + -
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Residues in contact with VAL 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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7A PHE* 4.3 6.3 - - + -
9A TYR* 4.3 15.5 - - + -
16A ILE* 4.0 22.0 - - + -
21A ILE* 3.6 31.0 - - + -
253A GLN 2.9 23.0 + - - +
254A TYR 3.9 3.1 - - - +
256A VAL* 1.3 76.5 - - - +
258A ARG* 1.3 62.4 + - - +
260A ALA* 3.1 2.9 + - - +
261A LEU* 3.0 29.0 + - + +
382A LEU* 3.8 35.4 - - + -
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Residues in contact with ARG 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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254A TYR* 2.9 47.7 + - + +
255A ALA* 3.4 14.1 - - - +
257A VAL* 1.3 77.1 - - - +
259A ASN* 1.3 63.7 + - - +
261A LEU* 3.4 3.2 + - - +
262A TYR* 3.0 23.4 + - - +
269A GLU* 2.8 31.1 + - - -
285A TRP* 4.8 1.8 - - - -
289A PHE* 3.5 31.5 - - - +
293A GLU* 2.8 21.8 + - - -
300A ILE* 3.5 36.6 + - + +
302A PRO* 5.8 1.4 - - - +
326A PHE* 3.8 24.2 - - + -
382A LEU* 5.3 0.2 - - + -
408A SER* 2.8 33.9 + - - +
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Residues in contact with ASN 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 ALA 3.0 28.8 + - - +
256A VAL* 3.8 5.6 - - - +
257A VAL 3.2 0.2 - - - -
258A ARG* 1.3 78.1 - - - +
260A ALA* 1.3 60.4 + - - +
262A TYR* 3.4 9.0 + - - +
263A ASN* 3.1 32.2 + - - +
300A ILE* 5.3 1.3 - - - -
408A SER* 3.1 36.2 + - - +
411A LEU* 4.0 14.7 - - + +
412A LEU* 3.6 33.8 + - - +
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Residues in contact with ALA 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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16A ILE* 3.7 21.1 - - + -
20A GLU* 3.9 7.4 - - + +
256A VAL* 2.9 20.5 + - + +
257A VAL 3.1 4.7 + - - +
259A ASN* 1.3 77.9 - - - +
261A LEU* 1.3 61.7 + - - +
263A ASN* 3.2 9.5 + - - +
264A LYS* 3.2 25.9 + - - +
298D LYS* 3.6 23.5 - - - +
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Residues in contact with LEU 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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12A ALA* 6.3 0.2 - - + -
15A PHE* 4.8 2.9 - - + -
16A ILE* 4.6 14.8 - - + -
257A VAL* 3.0 33.8 + - + +
258A ARG 3.8 3.8 - - - +
260A ALA* 1.3 72.3 - - - +
262A TYR* 1.3 65.8 + - - +
264A LYS* 3.0 34.2 + - + +
266A LYS* 2.9 33.7 + - + +
326A PHE* 3.6 43.5 - - + -
380A PRO* 4.0 27.4 - - + -
382A LEU* 4.4 6.1 - - + -
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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 ARG 3.0 14.5 + - - +
259A ASN* 3.5 12.6 - - - +
260A ALA 3.3 0.2 - - - -
261A LEU* 1.3 75.6 - - - +
263A ASN* 1.3 61.9 + - - +
265A GLY* 3.0 21.0 + - - -
266A LYS 3.4 9.1 + - - -
267A THR* 3.9 14.5 - - + +
299A GLY* 3.1 38.3 + - - -
300A ILE* 3.5 25.8 - - + -
412A LEU* 3.9 17.7 - - + -
322B ARG* 2.8 27.6 + - - -
322C ARG* 5.0 2.1 + - - -
262D TYR* 5.6 0.2 - - - -
263D ASN* 2.6 53.9 + - - -
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Residues in contact with ASN 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 ASN* 3.1 23.8 + - - +
260A ALA* 3.5 11.4 - - - +
261A LEU 3.2 0.2 - - - -
262A TYR* 1.3 78.1 - - - +
264A LYS* 1.3 56.7 + - - +
265A GLY 3.2 1.4 + - - -
322C ARG* 3.6 3.0 + - - -
262D TYR* 2.6 41.6 + - + -
263D ASN* 3.3 26.1 + - - +
298D LYS* 3.6 21.6 - - + +
411D LEU 5.5 1.2 + - - -
412D LEU* 3.8 27.8 + - + +
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Residues in contact with LYS 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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15A PHE* 2.9 29.8 + - + +
16A ILE* 4.3 2.7 - - - +
20A GLU* 2.9 35.3 + - - -
260A ALA 3.2 14.1 + - - +
261A LEU* 3.0 29.3 + - + +
263A ASN* 1.3 76.5 - - - +
265A GLY* 1.3 58.0 + - - +
266A LYS* 3.5 14.9 + - + +
322C ARG* 3.7 11.6 + - - -
323C ARG 5.5 2.3 + - - -
296D ASP 2.7 36.5 + - - +
297D GLN* 3.3 28.7 + - + +
298D LYS* 3.9 3.8 - - + -
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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