Contacts of the helix formed by residues 369 - 390 (chain B) in PDB entry 2IG7
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 GLY 369 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B TRP* 3.6 12.4 - - - -
294B PRO* 2.9 28.3 + - - -
296B TYR* 4.2 1.7 - - - -
368B PHE* 1.3 73.3 - - - +
370B TYR* 1.3 53.3 - - - -
371B LEU 3.4 2.5 - - - -
372B ASP* 3.2 3.6 + - - +
373B TYR* 2.8 35.0 + - - +
1003B UNX 3.4 15.0 - - - -
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Residues in contact with TYR 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 2.7 28.4 + - + -
356B TRP* 3.8 20.2 - + - -
357B SER* 2.5 43.6 + - - +
360B GLN* 3.5 30.5 - - + -
361B ALA* 3.8 12.8 - - + +
364B SER* 2.9 32.0 + - - -
366B ILE* 3.5 25.8 - - - +
368B PHE* 2.9 45.0 + + + -
369B GLY* 1.3 70.7 - - - +
371B LEU* 1.3 57.7 + - - +
373B TYR 3.4 0.5 + - - -
374B ALA* 2.9 17.2 + - - +
1003B UNX 3.8 0.6 - - - -
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Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B MSE 6.1 1.3 - - - +
212B LEU* 4.1 8.1 - - + +
358B ILE* 4.2 27.8 - - + -
361B ALA* 3.5 28.7 - - + -
369B GLY 3.4 0.6 - - - -
370B TYR* 1.3 73.4 - - - +
372B ASP* 1.3 60.4 + - - +
374B ALA* 3.3 4.4 + - - +
375B GLN* 3.0 43.9 + - - +
1003B UNX 3.5 9.0 - - - -
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Residues in contact with ASP 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B TRP* 5.2 2.9 - - - +
294B PRO* 3.5 23.3 - - + +
296B TYR* 2.7 33.4 + - - -
369B GLY 3.5 7.6 - - - +
371B LEU* 1.3 74.3 - - - +
373B TYR* 1.3 63.0 + - - +
375B GLN* 3.3 19.9 + - - +
376B SER* 3.1 17.7 + - - -
1003B UNX 3.2 13.8 - - - -
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Residues in contact with TYR 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 5.7 1.6 - - + -
283B GLU* 4.4 1.0 + - - -
286B TYR* 3.7 24.2 - + - -
288B TYR* 2.8 33.0 + + - -
296B TYR* 3.6 24.1 + + + -
353B TRP* 4.4 12.1 - + + +
356B TRP* 4.7 11.0 - + - -
357B SER* 3.4 24.7 - - - -
368B PHE* 3.5 27.8 - + + -
369B GLY 2.8 16.4 + - - +
370B TYR 3.6 2.2 - - - +
372B ASP* 1.3 74.9 - - - +
374B ALA* 1.3 63.6 + - - +
376B SER* 3.2 3.6 + - - -
377B ARG* 3.0 63.4 + - + +
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Residues in contact with ALA 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B LEU* 3.9 6.3 - - + -
354B GLY* 3.6 26.0 - - - +
357B SER* 3.8 9.1 + - - -
358B ILE* 3.7 20.0 - - + +
370B TYR 2.9 17.6 + - - +
371B LEU* 3.3 10.9 + - - +
373B TYR* 1.3 70.9 - - - +
375B GLN* 1.3 63.9 + - - +
377B ARG* 3.3 2.4 + - - +
378B PHE* 3.0 31.1 + - + -
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Residues in contact with GLN 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B MSE 4.6 17.5 - - - +
212B LEU* 3.6 30.7 - - + +
215B MSE 6.1 0.4 - - - -
216B TYR* 4.5 9.3 + - + +
371B LEU* 3.0 30.8 + - - +
372B ASP* 3.4 20.0 - - - +
374B ALA* 1.3 75.6 - - - +
376B SER* 1.3 57.8 + - - +
378B PHE* 3.3 1.7 + - - +
379B GLN* 2.9 51.9 + - - +
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Residues in contact with SER 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B TYR* 3.0 29.9 + - - -
296B TYR* 3.6 20.6 - - - -
298B ALA* 3.9 10.6 - - - +
372B ASP 3.1 6.0 + - - -
373B TYR* 3.3 9.2 - - - -
375B GLN* 1.3 76.3 - - - +
377B ARG* 1.3 58.0 + - - +
379B GLN* 3.4 11.5 + - - +
380B PHE* 2.9 30.5 + - - +
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Residues in contact with ARG 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ASN* 5.0 0.2 + - - -
282B CYS* 3.4 13.6 - - - +
283B GLU* 4.5 7.9 + - - -
286B TYR* 3.4 34.2 - - - -
349B SER* 2.9 27.5 + - - -
350B HIS* 3.2 65.5 + - - +
353B TRP* 3.6 20.2 - - - +
354B GLY* 4.0 13.9 - - - +
373B TYR* 3.0 54.2 + - + +
374B ALA 3.3 6.5 + - - +
376B SER* 1.3 78.0 - - - +
378B PHE* 1.3 56.9 + - - +
380B PHE* 3.3 2.0 + - - -
381B TYR 2.8 23.9 + - - -
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Residues in contact with PHE 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B LEU* 4.9 2.7 - - + -
216B TYR* 4.0 28.5 - + + -
218B LEU* 3.5 39.7 - - + -
350B HIS 4.7 0.2 - - - -
351B PHE* 3.8 38.8 - + - -
354B GLY* 3.4 17.5 - - - -
355B LEU* 3.4 25.6 - - + -
358B ILE* 3.7 19.5 - - + -
374B ALA* 3.0 28.1 + - + +
375B GLN* 4.0 1.3 - - - +
377B ARG* 1.3 75.8 - - - +
379B GLN* 1.3 62.4 + - - +
381B TYR* 3.3 7.1 - + + +
382B PHE* 3.0 33.7 + + + -
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Residues in contact with GLN 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B MSE 5.6 0.2 - - - +
216B TYR* 3.0 29.5 + - + +
375B GLN* 2.9 37.0 + - - +
376B SER* 3.7 11.3 - - - +
378B PHE* 1.3 75.9 - - - +
380B PHE* 1.3 55.9 + - - +
382B PHE* 3.4 7.4 + - - +
383B GLN* 2.9 28.7 + - - +
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Residues in contact with PHE 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B CYS 5.2 0.9 - - - -
285B VAL* 3.6 37.9 - - + -
286B TYR* 3.7 16.6 - + - +
300B PRO* 4.2 15.9 - - + -
303B TYR* 4.1 13.7 - + + -
350B HIS* 3.2 27.4 - + + +
376B SER 2.9 18.4 + - - +
377B ARG 3.7 3.8 - - - +
379B GLN* 1.3 73.0 - - - +
381B TYR* 1.3 60.5 + - - +
383B GLN* 3.2 36.9 + - - -
384B GLN* 2.8 56.1 + - + +
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Residues in contact with TYR 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLU* 2.7 48.0 + - + +
225B LEU* 3.7 26.6 - - + +
228B LEU* 6.1 0.2 - - - +
347B LEU* 3.3 51.1 - - + +
350B HIS* 3.7 16.9 - - + -
351B PHE* 3.9 21.8 - + + -
377B ARG 2.8 14.8 + - - +
378B PHE* 3.3 15.3 - + + +
380B PHE* 1.3 74.7 - - - +
382B PHE* 1.3 82.2 + + - +
384B GLN 3.4 0.2 + - - -
385B LYS* 2.9 41.7 + - + +
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Residues in contact with PHE 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TYR* 3.6 51.6 - + + -
218B LEU* 5.4 2.7 - - + -
221B GLU* 3.8 33.0 - - + -
378B PHE* 3.0 25.6 + + + +
379B GLN* 3.9 5.2 - - - +
381B TYR* 1.3 94.4 - + - +
383B GLN* 1.3 60.2 + - - +
385B LYS* 3.6 13.2 - - + +
386B GLY* 2.8 27.9 + - - -
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Residues in contact with GLN 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PRO* 4.3 17.5 + - - +
379B GLN 2.9 14.6 + - - +
380B PHE* 3.4 36.7 - - - +
382B PHE* 1.3 74.5 - - - +
384B GLN* 1.3 57.7 + - - +
386B GLY* 3.1 3.4 + - - -
387B GLN* 2.9 53.7 + - + +
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Residues in contact with GLN 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TYR* 3.4 44.7 - - - -
343B SER 5.2 1.7 - - - +
346B ALA* 3.9 16.0 - - - +
347B LEU* 3.5 18.1 - - + +
350B HIS* 2.9 28.1 + - - +
380B PHE* 2.8 34.4 + - + +
383B GLN* 1.3 75.8 - - - +
385B LYS* 1.3 64.1 + - - +
387B GLN* 3.2 16.8 + - - +
388B LEU* 3.0 26.9 + - + +
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Residues in contact with LYS 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLU* 2.6 37.4 + - - +
224B ASN* 4.0 16.3 - - - +
228B LEU* 6.1 3.6 - - + -
347B LEU* 3.7 21.4 - - + +
381B TYR* 2.9 31.1 + - + +
382B PHE* 3.6 16.9 - - + +
384B GLN* 1.3 75.7 - - - +
386B GLY* 1.3 62.4 + - - +
388B LEU* 3.1 15.7 + - + +
389B THR* 3.2 24.4 + - + +
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Residues in contact with GLY 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B PHE 2.8 15.6 + - - -
383B GLN* 3.5 4.7 - - - -
385B LYS* 1.3 77.4 - - - +
387B GLN* 1.3 57.9 + - - +
389B THR* 2.8 26.7 + - - -
390B SER* 3.5 7.8 + - - -
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Residues in contact with GLN 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLN* 2.9 46.7 + - + +
384B GLN* 3.6 20.3 + - - +
385B LYS 3.2 0.2 - - - -
386B GLY* 1.3 75.5 - - - +
388B LEU* 1.3 63.2 + - + +
389B THR 3.4 0.2 - - - -
390B SER* 3.6 20.7 - - - -
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Residues in contact with LEU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU* 4.5 7.4 - - + -
343B SER* 3.5 36.6 - - - +
344B ARG* 4.1 22.4 - - + +
347B LEU* 3.6 30.5 - - + -
384B GLN* 3.0 16.0 + - + +
385B LYS* 3.1 9.4 + - + +
387B GLN* 1.3 74.6 - - + +
389B THR* 1.3 67.2 + - + +
390B SER 3.2 9.6 + - - -
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Residues in contact with THR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B LYS* 3.2 25.4 - - + +
386B GLY* 2.8 21.7 + - - +
388B LEU* 1.3 77.2 - - + +
390B SER* 1.3 59.4 + - - +
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Residues in contact with SER 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B GLY 3.5 12.8 + - - -
387B GLN* 3.6 15.8 + - - -
388B LEU 3.3 12.3 - - - -
389B THR* 1.3 84.8 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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