Contacts of the helix formed by residues 365 - 380 (chain D) in PDB entry 1I3O
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 GLU 365 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368B HIS* 2.9 33.0 + - + +
364D LEU* 1.3 75.7 - - - +
366D PHE* 1.3 82.7 + - - +
367D MET* 3.0 34.6 + - - +
368D HIS* 3.1 11.2 + - - +
369D ILE* 3.0 20.1 + - - +
394D LEU* 5.4 1.4 - - - +
396D LYS 4.9 0.7 - - - +
397D GLU* 3.5 29.2 - - + -
398D LEU* 2.8 28.0 + - - +
399D TYR* 3.7 25.4 - - + +
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Residues in contact with PHE 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C PHE* 6.0 1.8 - + - -
279C LEU* 3.4 28.0 - - + -
281C ILE* 5.2 12.6 - - + -
328D LEU* 3.2 36.3 - - + -
330D ALA* 5.5 2.9 - - + -
353D LEU* 5.2 1.1 - - + -
357D LEU* 4.1 16.8 - - + -
364D LEU 3.8 0.6 + - - -
365D GLU* 1.3 77.8 + - - +
367D MET* 1.3 59.6 + - + +
369D ILE* 2.9 15.1 + - + +
370D LEU* 2.8 59.9 + - + +
394D LEU* 5.2 0.4 - - + -
398D LEU* 2.9 32.2 + - + +
400D PHE* 3.5 28.3 - + + -
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Residues in contact with MET 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B MET* 4.2 35.4 - - + +
368B HIS* 5.0 0.9 - - + -
371B THR* 4.8 11.0 - - + +
389B ILE* 6.1 0.9 - - - -
328D LEU* 3.4 39.5 - - + -
365D GLU* 3.0 22.7 + - - +
366D PHE* 1.3 82.9 - - + +
368D HIS* 1.3 54.2 + - + +
370D LEU* 3.3 11.0 + - + +
371D THR* 2.6 37.4 + - - -
389D ILE* 4.1 14.3 - - + +
392D SER* 3.9 22.7 - - - +
394D LEU* 4.3 9.4 - - + -
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Residues in contact with HIS 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B GLU* 2.9 38.0 + - + +
367B MET* 4.8 0.9 - - + -
368B HIS* 3.2 39.1 + + - -
397B GLU* 3.4 37.7 + - + +
399B TYR* 4.5 3.1 - - - -
364D LEU* 4.6 17.1 - - + +
365D GLU* 3.1 17.7 + - - +
367D MET* 1.3 78.7 - - + +
369D ILE* 1.3 65.7 + - - +
371D THR* 3.1 9.7 + - - -
372D ARG* 3.0 26.6 + - - +
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Residues in contact with ILE 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D MET* 3.9 32.1 - - + +
357D LEU* 4.1 17.5 - - + +
360D TYR* 4.1 15.9 - - + +
361D ALA* 4.1 13.5 - - - -
364D LEU* 3.4 33.7 - - + +
365D GLU 3.0 11.8 + - - +
366D PHE* 2.9 22.8 + - + +
368D HIS* 1.3 76.8 - - - +
370D LEU* 1.3 56.7 + - + +
372D ARG* 2.8 35.6 + - - +
373D VAL* 3.0 10.9 + - + +
400D PHE* 4.7 5.2 - - + -
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Residues in contact with LEU 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D LEU* 4.1 11.2 - - + -
330D ALA* 4.1 24.5 - - + -
349D PHE* 5.2 4.7 - - + -
353D LEU* 3.6 31.2 - - + -
366D PHE* 2.8 58.1 + - + +
367D MET* 3.8 8.3 - - + +
369D ILE* 1.3 74.1 - - + +
371D THR* 1.3 58.4 + - - +
373D VAL* 3.4 10.8 + - + +
374D ASN* 3.1 30.3 + - - +
389D ILE* 3.5 25.7 - - + +
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Residues in contact with THR 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B MET* 4.8 11.8 - - - +
392B SER* 5.1 2.8 + - - -
394B LEU* 3.7 12.3 - - + +
395B THR 3.4 29.7 - - - +
396B LYS* 3.8 18.8 - - - +
397B GLU* 4.6 5.6 - - + +
367D MET 2.6 25.4 + - - -
368D HIS* 3.5 12.8 - - - -
369D ILE 3.0 0.2 - - - -
370D LEU* 1.3 75.6 - - - +
372D ARG* 1.3 66.4 + - - +
374D ASN* 3.5 4.8 + - - +
375D ARG 3.3 14.7 + - - -
389D ILE* 4.1 10.2 - - - +
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Residues in contact with ARG 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A SER* 4.9 10.3 + - - -
151A ASN* 4.0 25.1 - - - +
395B THR 5.3 0.2 - - - -
397B GLU* 5.6 3.4 + - - -
356D MET* 3.1 33.5 - - + +
360D TYR* 3.3 41.8 + - + -
364D LEU* 4.0 14.3 - - + +
368D HIS 3.0 17.1 + - - +
369D ILE* 2.8 16.3 + - - +
371D THR* 1.3 79.6 - - - +
373D VAL* 1.3 55.8 + - - +
375D ARG* 3.1 37.4 + - - +
376D LYS* 2.8 28.4 + - - +
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Residues in contact with VAL 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349D PHE* 4.1 28.7 - - + -
352D SER* 3.7 21.1 - - - -
353D LEU* 3.8 18.6 - - + +
356D MET* 3.8 23.8 - - + -
369D ILE* 3.3 16.2 - - + +
370D LEU* 3.5 22.7 - - + +
372D ARG* 1.3 74.3 - - - +
374D ASN* 1.3 66.1 + - - +
376D LYS* 3.6 3.3 - - - +
377D VAL* 2.8 26.2 + - + +
387D PRO* 4.8 1.1 - - + -
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Residues in contact with ASN 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B SER* 3.6 9.5 + - - -
393B MET* 3.6 20.6 - - - +
394B LEU 3.0 29.5 + - - +
395B THR* 3.9 2.5 - - - -
349D PHE* 5.4 0.2 - - - -
370D LEU 3.1 16.5 + - - +
371D THR* 3.6 5.4 - - - +
372D ARG 3.2 0.2 - - - -
373D VAL* 1.3 78.0 - - - +
375D ARG* 1.3 57.1 + - - +
378D ALA* 2.9 32.1 + - - +
386D ILE* 4.0 6.0 - - + +
387D PRO* 3.1 40.7 + - - +
389D ILE* 3.6 17.2 - - - +
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Residues in contact with ARG 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A SER* 5.5 1.0 + - - -
149A LEU 5.3 2.4 + - - -
150A ASP 3.9 16.3 + - - -
151A ASN* 3.7 16.0 + - - +
395B THR* 3.3 40.8 + - - +
396B LYS* 4.2 19.4 - - - +
356D MET* 6.0 0.4 - - - +
371D THR 3.3 3.5 + - - +
372D ARG* 3.1 46.0 + - - +
374D ASN* 1.3 77.7 - - - +
376D LYS* 1.3 57.6 + - - +
379D THR* 2.7 55.5 + - - +
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Residues in contact with LYS 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D GLN* 5.3 4.3 - - - +
352D SER* 3.2 34.5 + - - +
355D ALA* 3.9 22.2 - - - -
356D MET* 4.3 16.4 - - + -
359D GLN* 6.1 0.4 - - - -
372D ARG 2.8 16.9 + - - +
373D VAL* 3.2 5.6 + - - +
375D ARG* 1.3 76.5 - - - +
377D VAL* 1.3 58.6 + - - +
379D GLU* 2.6 79.7 + - + +
380D PHE* 3.6 10.1 - - + -
232F GLY 4.0 9.9 + - - -
233F ARG* 4.9 2.4 - - - +
234F ASN 5.4 1.4 - - - +
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Residues in contact with VAL 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D TRP* 4.0 21.3 - - + +
349D PHE* 4.1 8.5 - - - -
352D SER* 3.5 22.9 - - - +
373D VAL* 2.8 21.0 + - + +
376D LYS* 1.3 76.0 - - - +
378D ALA* 1.3 61.9 + - - +
379D THR 3.4 0.2 + - - -
380D PHE* 3.5 28.3 + - - +
385D GLN* 3.5 38.8 + - + +
387D PRO* 3.6 26.9 - - + -
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Residues in contact with ALA 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B LYS 3.7 2.4 - - - +
321B ILE* 3.9 4.8 - - + -
322B PRO* 3.3 22.9 - - + +
325B ALA* 4.6 1.1 - - + -
395B THR* 3.9 11.9 - - + -
374D ASN 2.9 18.7 + - - +
375D ARG 3.8 2.5 - - - +
377D VAL* 1.3 77.5 - - - +
379D THR* 1.3 58.5 + - - +
384D LYS* 3.0 27.9 + - - -
385D GLN 3.6 9.6 + - - -
386D ILE* 3.8 17.7 - - + -
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Residues in contact with THR 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B HIS* 3.1 36.4 + - + +
321B ILE* 5.1 4.9 - - - +
395B THR* 5.9 0.2 - - - +
375D ARG* 2.7 38.7 + - + +
376D LYS 4.2 0.2 - - - -
378D ALA* 1.3 76.2 - - - +
379D GLU* 1.3 78.3 + - + +
380D PHE 3.4 1.2 + - - -
384D LYS* 3.7 4.2 + - - -
231F LEU* 3.8 18.2 - - + +
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Residues in contact with GLU 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376D LYS* 2.6 61.1 + - + +
379D THR* 1.3 86.6 - - + +
380D PHE* 1.3 61.5 + - + +
228F PHE* 5.4 0.5 - - - -
231F LEU* 3.2 48.7 + - + +
232F GLY* 3.3 14.2 - - - -
233F ARG* 2.7 37.2 + - + +
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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