Contacts of the helix formed by residues 320 - 333 (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 HIS 320 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B GLY 3.5 13.0 + - - +
85B ARG 2.9 27.8 - - - -
86B ALA 4.8 0.9 - - - +
87B ALA* 3.4 25.4 + - + +
318B ARG 3.2 7.3 + - - +
319B ILE* 1.3 75.4 - - - +
321B PRO* 1.3 76.7 - - + +
322B PHE* 3.1 36.8 - - + -
323B HIS* 3.2 34.9 + - + +
324B ILE* 3.4 10.6 + - - +
360B SER* 4.3 0.9 - - - -
522B PHE* 3.2 31.8 + - - -
524B SER* 3.5 18.4 + - - -
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Residues in contact with PRO 321 (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 ILE 3.8 0.4 - - - +
320B HIS* 1.3 106.4 - - + +
322B PHE* 1.3 57.6 + - - +
324B ILE* 3.0 8.2 + - + +
325B LEU 2.9 23.9 + - - -
357B PHE* 3.5 13.2 - - + -
360B SER* 3.6 25.4 - - - +
361B PHE* 3.4 50.0 - - + -
522B PHE* 3.6 5.4 - - + -
524B SER* 4.1 11.0 - - - -
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Residues in contact with PHE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ALA* 3.5 17.0 - - + -
88B LYS* 4.4 11.9 - - - -
320B HIS* 3.1 12.5 - - + -
321B PRO* 1.3 76.3 - - - +
323B HIS* 1.3 84.3 - + - +
325B LEU* 3.0 4.2 + - - +
326B VAL* 2.8 50.8 + - + +
385B VAL* 4.5 3.4 - - + -
386B LEU* 3.6 37.5 - - + -
388B SER* 3.7 22.9 - - - -
390B LEU* 4.6 8.7 - - + -
395B VAL* 5.5 4.5 - - + -
522B PHE* 3.0 33.9 - + + -
10F U 5.6 3.4 - - - -
11F U 5.1 1.8 - - - -
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Residues in contact with HIS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ALA 2.8 29.0 + - - -
88B LYS* 4.7 1.1 - - + -
279B THR* 5.8 7.2 - - + -
282B LEU* 3.8 18.1 - - + +
318B ARG 5.1 3.4 - - - -
319B ILE* 4.9 3.4 - - + -
320B HIS* 3.2 33.5 + - + +
322B PHE* 1.3 98.2 - + - +
324B ILE* 1.3 60.6 + - - +
326B VAL* 4.0 4.5 - - - +
327B ALA* 3.2 24.3 + - - +
9F U 4.7 1.6 - - - +
11F U 3.9 23.1 + - - -
13F C 6.1 3.9 - + - -
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Residues in contact with ILE 324 (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* 3.7 18.6 - - + -
308B LEU* 5.8 1.1 - - + -
314B LEU* 4.9 4.0 - - + -
319B ILE* 3.2 29.4 - - + -
320B HIS 3.4 13.9 - - - +
321B PRO* 3.0 12.5 + - + +
323B HIS* 1.3 76.0 - - - +
325B LEU* 1.3 60.9 + - - +
327B ALA* 3.2 4.1 + - - +
328B LEU* 2.8 30.4 + - + +
353B LEU* 3.4 37.8 - - + +
356B ALA* 4.5 12.6 - - + -
357B PHE* 3.8 17.7 - - + +
360B SER* 3.9 10.1 - - - +
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Residues in contact with LEU 325 (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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321B PRO 2.9 11.6 + - - +
322B PHE* 3.0 9.2 + - - +
324B ILE* 1.3 76.7 - - - +
326B VAL* 1.3 61.9 + - - +
328B LEU* 3.2 7.0 + - + +
329B GLU* 2.9 24.6 + - + +
357B PHE* 4.1 7.8 - - + -
390B LEU* 3.2 39.3 - - + -
394B VAL* 4.5 9.6 - - + -
395B VAL* 4.3 18.4 - - + -
398B ALA* 4.5 14.6 - - + -
430B LEU* 4.2 17.0 - - + -
434B VAL* 4.5 17.0 - - + -
522B PHE* 4.4 10.8 - - + -
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B PHE* 2.8 56.3 + - + +
323B HIS* 4.0 5.8 - - - +
325B LEU* 1.3 72.4 - - - +
327B ALA* 1.3 57.7 + - - +
329B GLU* 3.5 4.4 + - - +
330B THR* 3.0 29.1 + - - +
388B SER* 4.2 10.5 - - - -
389B ILE* 6.0 1.6 - - + +
390B LEU* 3.7 15.0 - - + +
9F U 3.3 28.0 - - - +
10F U 3.4 17.3 - - - +
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU* 4.1 20.9 - - + +
285B LEU* 5.3 0.4 - - + -
323B HIS 3.2 16.0 + - - +
324B ILE 3.7 2.9 - - - +
326B VAL* 1.3 75.8 - - - +
328B LEU* 1.3 58.3 + - - +
330B THR* 4.8 0.2 - - - -
331B TYR* 2.7 39.9 + - - +
353B LEU* 4.2 6.1 - - + -
9F U 3.3 38.4 + - + +
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Residues in contact with LEU 328 (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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324B ILE* 2.8 22.6 + - + +
325B LEU* 3.6 7.9 - - + +
327B ALA* 1.3 74.6 - - - +
329B GLU* 1.3 64.4 + - + +
331B TYR* 3.9 0.2 - - - +
332B LYS* 3.0 31.1 + - + +
350B VAL* 3.8 13.9 - - + +
353B LEU* 3.7 20.6 - - + +
354B ASP* 3.2 48.7 - - + +
357B PHE* 6.2 0.2 - - + -
430B LEU* 4.6 9.6 - - + -
431B HIS* 3.5 39.9 - - + +
434B VAL* 5.4 4.0 - - + -
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Residues in contact with GLU 329 (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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325B LEU* 2.9 18.2 + - + +
326B VAL* 3.7 4.5 - - - +
328B LEU* 1.3 79.8 - - - +
330B THR* 1.3 62.1 + - - +
332B LYS* 2.8 47.1 + - - +
333B LYS* 2.7 42.8 + - - +
389B ILE* 5.1 10.1 - - + +
390B LEU* 3.9 24.7 - - + -
434B VAL* 3.8 21.5 - - + +
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Residues in contact with THR 330 (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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326B VAL* 3.0 19.5 + - - +
329B GLU* 1.3 75.3 - - - +
331B TYR* 1.3 67.1 + - - +
333B LYS* 3.3 21.8 + - + +
335B HIS 3.4 6.1 - - - +
336B GLY* 3.8 24.2 - - - -
337B ASN* 4.5 2.5 + - - +
343B TRP* 3.5 6.3 - - + -
389B ILE* 5.2 7.6 - - - +
9F U 3.7 54.4 + - + +
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Residues in contact with TYR 331 (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 21.5 - - + -
286B GLY* 3.7 14.8 - - - -
289B THR* 2.7 29.6 + - - -
327B ALA 2.7 25.6 + - - +
328B LEU 3.9 2.0 - - - +
330B THR* 1.3 72.9 - - - +
332B LYS* 1.3 63.7 + - - +
334B GLY 3.2 2.1 + - - -
343B TRP* 2.7 46.1 + + - +
345B PRO* 3.5 8.8 - - + +
346B ASP* 3.2 40.9 + - - +
349B ILE* 3.5 37.5 - - + +
350B VAL* 4.0 12.6 - - + -
353B LEU* 4.3 10.1 - - + -
9F U 4.2 5.3 - - - +
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Residues in contact with LYS 332 (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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328B LEU* 3.0 17.8 + - + +
329B GLU* 2.8 42.7 + - - +
331B TYR* 1.3 73.2 - - - +
333B LYS* 1.3 58.2 + - + +
334B GLY 3.0 9.8 + - - -
345B PRO* 3.7 21.5 - - + +
350B VAL* 4.4 17.0 - - + -
431B HIS* 2.8 72.7 + - + +
434B VAL* 4.4 3.4 - - - +
435B GLU* 5.1 5.5 + - - +
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Residues in contact with LYS 333 (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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329B GLU* 2.7 41.7 + - - +
330B THR* 3.3 16.1 + - - +
331B TYR 3.1 0.6 - - - -
332B LYS* 1.3 83.1 - - + +
334B GLY* 1.3 51.8 + - - +
335B HIS* 2.7 56.9 + - + +
336B GLY 5.8 1.8 - - - +
337B ASN* 6.4 1.6 - - + -
389B ILE* 5.7 6.9 - - - +
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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