Contacts of the helix formed by residues 349 - 360 (chain B) in PDB entry 2IIK
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 PHE 349 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B MET* 3.6 26.2 - - + -
183B GLY* 3.6 33.2 - - - -
186B SER* 3.5 22.0 - - - +
265B PHE* 4.0 11.7 - + - -
271B THR* 3.6 11.4 - - + -
275B ASN 3.8 5.8 - - - +
276B SER* 3.4 28.3 - - - -
277B SER* 5.7 1.6 - - - -
318B MET* 4.3 12.6 - - + -
347B GLU 4.2 5.6 - - - -
348B ALA* 1.3 99.5 - - + +
350B ALA* 1.3 65.1 + - - +
351B SER* 3.5 6.7 - - - +
352B GLN* 3.1 11.1 + - + +
353B ALA* 3.0 21.4 + - - +
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Residues in contact with ALA 350 (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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200B GLN* 3.4 33.2 - - + +
203B PHE* 3.9 25.1 - - + -
204B ALA* 4.7 1.6 - - + +
275B ASN* 2.8 29.2 + - + +
349B PHE* 1.3 71.2 - - - +
351B SER* 1.3 57.1 + - - +
353B ALA* 4.4 1.8 - - - -
354B ALA* 2.8 35.7 + - - +
374B VAL* 4.5 3.7 - - + +
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Residues in contact with SER 351 (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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186B SER* 2.7 45.6 + - - -
189B VAL* 4.5 2.9 - - - +
190B ALA* 4.2 11.0 - - - -
195B ILE* 4.2 9.4 - - - +
200B GLN* 3.7 31.6 - - - +
349B PHE* 3.5 5.4 - - - +
350B ALA* 1.3 77.9 - - - +
352B GLN* 1.3 64.2 + - - +
354B ALA* 3.7 1.6 - - - +
355B TYR* 2.9 30.0 + - - +
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Residues in contact with GLN 352 (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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186B SER* 5.7 2.5 - - - -
189B VAL* 4.2 15.3 - - + -
318B MET* 5.2 1.1 - - + -
319B GLY* 2.9 44.2 + - - +
322B PRO* 4.6 5.7 - - - +
345B ILE* 4.6 6.3 - - - +
346B ASN 3.3 19.0 + - - -
348B ALA* 3.3 14.0 + - - +
349B PHE* 3.1 34.0 + - + +
351B SER* 1.3 81.6 + - - +
353B ALA* 1.3 81.5 + - - +
355B TYR* 3.5 2.3 + - - +
356B CYS* 3.1 29.5 + - - -
409B CYS* 3.5 17.1 - - - +
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Residues in contact with ALA 353 (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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203B PHE* 3.5 32.3 - - + -
345B ILE* 4.8 6.8 - - + +
346B ASN 4.2 10.8 - - - +
347B GLU* 4.2 5.6 - - + -
349B PHE 3.0 16.2 + - - +
350B ALA 4.0 0.4 - - - +
352B GLN* 1.3 88.2 - - - +
354B ALA* 1.3 64.8 + - - +
356B CYS* 3.3 5.3 + - - +
357B VAL* 3.1 27.3 + - + +
368B ASN* 5.8 0.2 - - - +
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Residues in contact with ALA 354 (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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195B ILE* 4.3 16.2 - - + -
199B LYS* 4.8 13.5 - - + +
200B GLN* 5.7 0.2 - - - -
203B PHE* 4.1 22.8 - - + -
350B ALA 2.8 19.3 + - - +
351B SER 3.7 2.7 - - - +
353B ALA* 1.3 74.6 - - - +
355B TYR* 1.3 67.5 + - - +
357B VAL* 3.3 4.9 + - - +
358B GLU* 3.1 30.8 + - - +
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Residues in contact with TYR 355 (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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189B VAL* 4.3 6.1 - - + -
193B PHE* 3.6 49.6 - + + -
195B ILE* 4.3 16.1 - - + +
320B ILE* 3.5 37.2 - - + -
323B ALA* 4.4 5.8 - - + -
324B TYR* 4.6 6.4 + + - -
351B SER 2.9 18.6 + - - +
352B GLN 3.7 4.3 - - - +
353B ALA 3.3 0.2 - - - -
354B ALA* 1.3 79.4 - - - +
356B CYS* 1.3 64.3 + - - +
358B GLU* 3.2 5.9 + - + +
359B LYS* 2.8 75.9 + - + +
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Residues in contact with CYS 356 (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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319B GLY 3.6 19.7 - - - -
320B ILE* 3.8 9.9 - - - -
322B PRO* 3.8 19.1 - - + -
323B ALA* 3.6 28.0 - - - +
345B ILE* 4.8 9.6 - - + -
352B GLN* 3.1 18.7 + - - +
353B ALA* 3.6 6.7 - - - +
355B TYR* 1.3 83.3 - - - +
357B VAL* 1.3 62.4 + - - +
359B LYS* 4.6 2.9 - - - -
360B LEU* 3.1 33.0 + - + +
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Residues in contact with VAL 357 (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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203B PHE* 4.6 10.1 - - + -
345B ILE* 4.5 8.7 - - + -
353B ALA* 3.1 17.1 + - + +
354B ALA* 3.8 7.4 - - - +
356B CYS* 1.3 74.9 - - - +
358B GLU* 1.3 62.3 + - + +
360B LEU 3.8 0.2 - - - -
361B ARG* 3.0 21.8 + - - -
362B LEU* 3.1 42.1 + - + +
364B PRO* 4.8 12.6 - - + -
367B VAL* 3.8 35.4 - - + -
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Residues in contact with GLU 358 (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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195B ILE* 5.2 5.9 - - - +
199B LYS* 3.2 42.4 + - - +
354B ALA* 3.1 21.6 + - - +
355B TYR* 3.8 5.3 - - + +
357B VAL* 1.3 79.6 - - + +
359B LYS* 1.3 66.1 + - - +
361B ARG* 3.0 22.2 + - - +
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Residues in contact with LYS 359 (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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323B ALA* 4.1 18.4 - - + +
324B TYR* 4.1 17.6 + - + -
355B TYR* 2.8 58.8 + - + +
356B CYS 4.0 2.9 - - - +
358B GLU* 1.3 73.1 - - - +
360B LEU* 1.3 65.0 + - + +
361B ARG* 3.5 10.6 + - - -
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Residues in contact with LEU 360 (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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322B PRO 3.8 11.7 - - - +
323B ALA* 3.6 28.0 - - + +
326B ILE* 3.8 38.4 - - + -
327B PRO* 3.9 17.3 - - + -
337B VAL* 4.5 14.0 - - + +
345B ILE* 5.1 1.3 - - + -
356B CYS 3.1 19.1 + - - +
359B LYS* 1.3 81.3 - - + +
361B ARG* 1.3 72.1 + - - +
362B LEU* 3.3 26.0 + - + +
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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