Contacts of the helix formed by residues 346 - 360 (chain B) in PDB entry 2I91
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 346 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B THR* 4.8 5.6 - - + +
294B LEU* 4.6 3.7 - - + +
296B PRO* 3.8 27.7 - - - +
297B ALA 4.8 0.9 + - - -
301B VAL* 3.7 14.9 - - + +
331B TYR* 3.2 19.8 + - - +
344B ILE 3.1 5.6 + - - +
345B PRO* 1.3 70.5 - - - +
347B THR* 1.3 63.3 + - - +
348B SER* 2.9 39.0 + - - -
349B ILE* 3.3 16.6 + - + +
350B VAL* 3.2 23.7 + - - +
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Residues in contact with THR 347 (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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345B PRO 3.4 6.1 + - - -
346B ASP* 1.3 71.0 + - - +
348B SER* 1.3 63.8 + - - +
349B ILE 3.3 0.2 - - - -
350B VAL* 3.6 9.8 + - + +
351B GLU* 3.3 22.6 + - + +
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Residues in contact with SER 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B VAL* 4.2 8.5 - - - +
302B SER* 6.2 0.2 - - - -
305B CYS* 3.5 18.3 - - - -
346B ASP* 2.9 15.0 + - - -
347B THR* 1.3 78.6 - - - +
349B ILE* 1.3 56.5 + - - +
351B GLU* 3.4 15.6 + - - +
352B ALA* 3.0 26.9 + - - +
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Residues in contact with ILE 349 (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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285B LEU* 3.7 32.5 - - + -
294B LEU* 5.2 4.3 - - + -
301B VAL* 3.6 19.5 - - + -
304B VAL* 3.9 19.7 - - + -
305B CYS* 3.4 24.0 - - - -
308B LEU* 4.6 3.4 - - + -
331B TYR* 3.5 30.1 - - + +
346B ASP* 3.3 22.4 + - + +
348B SER* 1.3 72.7 - - - +
350B VAL* 1.3 58.9 + - - +
351B GLU 3.1 1.6 - - - -
352B ALA* 4.1 1.1 - - - -
353B LEU* 2.8 35.2 + - + +
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 3.8 11.7 - - + +
331B TYR* 4.0 19.3 - - + -
332B LYS* 4.4 16.6 - - + -
345B PRO* 4.6 7.4 - - + -
346B ASP 3.2 19.5 + - - +
347B THR* 4.0 10.3 - - + +
348B SER 3.4 0.2 - - - -
349B ILE* 1.3 76.5 - - - +
351B GLU* 1.3 57.9 + - - +
353B LEU* 4.7 5.2 - - - +
354B ASP* 3.1 29.1 + - + +
429B LEU* 6.6 0.2 - - + -
431B HIS* 4.1 27.1 - - + +
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Residues in contact with GLU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B CYS* 5.9 0.3 - - - -
347B THR* 3.3 16.8 + - + +
348B SER* 3.7 16.8 + - - +
349B ILE 3.1 0.6 - - - -
350B VAL* 1.3 80.0 - - - +
352B ALA* 1.3 57.9 + - - +
354B ASP* 3.9 12.5 - - - +
355B ASN* 3.2 31.6 + - - +
429B LEU* 5.4 7.9 - - + -
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Residues in contact with ALA 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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305B CYS* 3.8 33.2 - - + -
308B LEU* 4.6 8.3 - - + -
309B THR* 3.3 23.4 - - + +
348B SER 3.0 15.4 + - - +
349B ILE* 3.0 7.0 + - - +
351B GLU* 1.3 80.4 - - - +
353B LEU* 1.3 53.7 + - - +
355B ASN* 3.2 0.8 + - - -
356B ALA* 2.7 31.3 + - - +
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Residues in contact with LEU 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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282B LEU* 3.3 33.0 - - + -
285B LEU* 3.7 26.0 - - + -
308B LEU* 3.8 13.2 - - + -
324B ILE* 3.4 16.7 - - + +
327B ALA* 4.2 6.7 - - + +
328B LEU* 3.7 41.7 - - + +
331B TYR* 4.3 9.2 - - + -
349B ILE* 2.8 23.5 + - + +
350B VAL* 4.2 1.6 - - - +
352B ALA* 1.3 72.7 - - - +
354B ASP* 1.3 58.3 + - - +
355B ASN 2.9 4.0 - - - -
356B ALA* 2.8 20.7 + - + -
357B PHE 2.9 11.4 + - - -
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Residues in contact with ASP 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 3.2 18.7 - - + +
350B VAL* 3.1 18.4 + - + +
351B GLU* 3.9 12.3 - - - +
353B LEU* 1.3 79.7 - - - +
355B ASN* 1.3 59.7 + - - +
357B PHE* 3.8 9.3 - - - +
358B TYR* 3.6 22.7 - - - -
405B ARG* 5.3 2.8 + - - -
429B LEU* 3.0 31.3 - - + +
430B LEU* 3.3 33.7 + - + +
431B HIS 5.4 0.7 - - - +
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Residues in contact with ASN 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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309B THR* 4.1 10.6 - - + +
351B GLU* 3.2 26.7 + - - +
352B ALA* 3.2 6.0 + - - +
353B LEU 2.9 0.6 - - - -
354B ASP* 1.3 78.4 - - - +
356B ALA* 1.3 65.1 + - - +
357B PHE 3.1 2.5 + - - -
358B TYR* 3.3 17.3 + - - +
359B LYS* 3.7 29.6 + - - +
405B ARG* 6.0 2.0 - - - +
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Residues in contact with ALA 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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308B LEU* 2.9 31.6 - - + +
309B THR* 4.4 2.4 - - - +
314B LEU* 4.0 10.7 - - + +
324B ILE* 4.5 13.9 - - + -
352B ALA 2.7 15.1 + - - +
353B LEU* 2.8 10.5 + - + +
355B ASN* 1.3 76.6 - - - +
357B PHE* 1.3 64.1 + - - +
359B LYS* 2.9 16.6 + - - +
360B SER* 3.1 14.7 + - - -
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Residues in contact with PHE 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PRO* 3.5 33.9 - - + -
324B ILE* 3.8 13.4 - - + +
325B LEU* 4.1 15.3 - - + -
353B LEU 2.9 10.5 + - - +
354B ASP* 3.8 7.0 - - - +
355B ASN 3.1 0.4 - - - -
356B ALA* 1.3 76.6 - - - +
358B TYR* 1.3 77.7 + + - +
360B SER* 2.7 19.7 + - - -
361B PHE* 3.4 38.7 - + - -
398B ALA* 3.5 33.7 - - + -
430B LEU* 3.2 39.3 - - + -
522B PHE* 4.1 10.5 - + - -
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Residues in contact with TYR 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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354B ASP* 3.6 18.2 - - - -
355B ASN* 3.3 12.2 + - - +
356B ALA 3.2 0.6 - - - -
357B PHE* 1.3 90.9 - + - +
359B LYS* 1.3 62.3 + - + +
360B SER 3.3 0.6 + - - -
361B PHE* 4.0 5.1 + - - -
363B LEU* 3.0 27.3 - - - +
401B MET* 3.1 35.0 - - + +
402B LEU* 3.8 45.3 - - + +
405B ARG* 3.7 37.2 + - + -
428B MET 4.9 0.3 + - - -
430B LEU* 3.3 30.5 - - + +
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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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309B THR* 3.3 42.6 + - - +
311B GLU* 3.0 49.0 - - + +
314B LEU* 3.9 9.5 - - + +
315B LYS* 5.4 1.7 - - - +
355B ASN* 3.8 31.2 - - - +
356B ALA 2.9 7.6 + - - +
358B TYR* 1.3 79.1 - - + +
360B SER* 1.3 62.7 + - - +
361B PHE 3.3 3.4 + - - +
363B LEU* 4.3 9.9 - - + -
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Residues in contact with SER 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LEU* 4.6 11.6 - - - +
315B LYS* 5.7 8.2 - - - +
319B ILE* 3.3 28.9 - - - +
320B HIS 4.3 0.7 - - - -
321B PRO* 3.6 22.2 - - - +
324B ILE* 3.9 5.8 - - - +
356B ALA 3.1 10.8 + - - -
357B PHE* 2.7 21.0 + - - -
359B LYS* 1.3 75.3 - - - +
361B PHE* 1.3 61.3 + - - +
362B LYS* 4.0 1.4 + - - +
524B SER* 4.1 10.7 - - - -
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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