Contacts of the helix formed by residues 379 - 398 (chain B) in PDB entry 1M7X
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 ARG 379 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B TRP* 4.5 9.1 - - + -
145B PRO* 5.4 3.0 - - - +
146B ASN* 5.1 6.9 - - - +
354B THR* 5.2 1.4 + - - -
355B ASN 3.1 17.8 + - - -
356B LEU* 3.0 48.1 + - - +
376B ASN* 3.3 22.9 + - - +
377B TYR 3.3 0.4 - - - -
378B GLY* 1.3 77.1 - - - +
380B ARG* 1.3 68.9 + - - +
381B GLU* 3.8 12.7 + - - +
382B VAL* 3.1 17.9 + - + +
383B SER* 2.9 24.4 + - - -
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Residues in contact with ARG 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B HIS* 2.8 41.5 + - - +
378B GLY 3.5 4.6 + - - -
379B ARG* 1.3 71.2 - - - +
381B GLU* 1.3 64.9 + - - +
383B SER* 3.8 4.9 - - - -
384B ASN* 2.7 58.9 + - - +
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Residues in contact with GLU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TRP* 3.4 59.1 + - + +
172B SER 5.0 4.0 - - - +
206B TYR* 4.9 1.2 + - - -
357B TYR* 4.8 1.0 - - - -
379B ARG* 3.2 10.3 - - - +
380B ARG* 1.3 87.1 + - - +
382B VAL* 1.3 62.0 + - - +
384B ASN* 3.4 11.7 + - - +
385B PHE* 3.0 25.6 + - - +
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Residues in contact with VAL 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TRP* 4.7 2.7 - - + -
356B LEU 3.7 20.6 - - - +
357B TYR* 3.8 22.7 - - + +
375B TYR* 3.5 44.0 - - + +
376B ASN* 3.6 15.3 - - + +
377B TYR* 4.8 0.7 - - - -
379B ARG* 3.1 24.3 + - + +
381B GLU* 1.3 73.2 - - - +
383B SER* 1.3 66.7 + - - +
385B PHE* 2.9 10.6 + - + +
386B LEU* 2.9 25.2 + - + +
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Residues in contact with SER 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TYR 3.6 19.2 + - - -
379B ARG 2.9 16.9 + - - -
380B ARG* 3.8 6.5 - - - -
382B VAL* 1.3 76.6 - - - +
384B ASN* 1.3 56.6 + - - +
386B LEU* 4.6 0.9 - - - -
387B VAL* 2.7 53.3 + - - +
438B PHE* 4.2 16.5 - - - -
441B ASN* 4.9 6.4 + - - -
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Residues in contact with ASN 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B HIS* 3.4 42.1 + - - +
119B LEU* 5.9 0.3 - - - +
121B PRO* 3.7 16.1 - - + +
206B TYR* 5.2 0.4 - - - +
380B ARG* 2.7 57.8 + - - +
381B GLU* 3.5 11.9 - - - +
383B SER* 1.3 75.9 + - - +
385B PHE* 1.3 60.0 + - - +
387B VAL* 4.7 2.9 - - - +
388B GLY* 2.6 34.9 + - - +
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Residues in contact with PHE 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B PRO* 3.7 28.9 - - + -
206B TYR* 3.4 31.3 + + + +
305B LEU* 3.7 25.1 - - + -
306B TYR* 2.7 40.5 + + - -
348B LEU* 4.1 16.4 - - + -
357B TYR* 4.0 16.2 - + + -
375B TYR* 3.8 31.0 - + - -
381B GLU 3.0 14.3 + - - +
382B VAL* 2.9 13.7 + - - +
384B ASN* 1.3 75.8 - - - +
386B LEU* 1.3 69.4 + - + +
389B ASN* 3.1 13.2 + - + +
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Residues in contact with LEU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 4.5 9.2 - - + -
336B TRP* 3.2 13.4 - - + -
338B PRO* 4.3 14.8 - - + +
375B TYR* 3.9 29.2 - - + +
377B TYR* 3.3 41.5 - - + -
382B VAL* 2.9 21.1 + - + +
383B SER* 5.0 0.2 - - - -
385B PHE* 1.3 92.6 - - + +
387B VAL* 1.3 67.6 + - - +
388B GLY 3.1 1.6 - - - -
389B ASN* 2.9 17.1 + - + +
390B ALA 3.2 7.8 + - - -
438B PHE* 3.5 22.0 - - + -
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Residues in contact with VAL 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 4.6 9.2 - - + +
336B TRP* 4.9 1.1 - - - -
383B SER* 2.7 38.9 + - - +
384B ASN* 4.2 2.7 - - - +
386B LEU* 1.3 70.9 - - - +
388B GLY* 1.3 63.0 + - - +
390B ALA* 3.0 18.5 + - - +
391B LEU* 3.2 18.1 + - + +
438B PHE* 3.9 4.9 - - + -
441B ASN* 4.7 3.1 - - - +
442B THR* 3.7 30.3 - - - +
445B ILE* 3.9 41.1 - - + -
446B LEU* 4.6 4.6 - - + +
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Residues in contact with GLY 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU 3.4 21.7 + - - -
121B PRO* 4.1 3.1 - - - -
122B TYR* 3.0 15.2 - - - -
306B TYR* 3.5 8.3 - - - -
384B ASN 2.6 23.2 + - - -
387B VAL* 1.3 74.0 - - - +
389B ASN* 1.3 51.3 + - - +
391B LEU* 3.1 2.4 + - - -
392B TYR* 2.8 31.5 + - - +
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Residues in contact with ASN 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 3.1 38.3 + - + +
306B TYR* 3.1 36.2 + - + -
336B TRP* 2.9 25.0 + - - +
385B PHE* 3.1 15.5 + - + +
386B LEU* 2.9 14.6 + - - +
388B GLY* 1.3 75.7 - - - +
390B ALA* 1.3 58.8 + - - +
392B TYR* 3.9 1.6 - - - -
393B TRP* 3.0 45.3 + - - +
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Residues in contact with ALA 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B TRP* 3.8 22.0 - - + +
386B LEU 3.2 3.4 + - - -
387B VAL* 3.0 10.8 + - - +
389B ASN* 1.3 76.1 - - - +
391B LEU* 1.3 66.1 + - - +
393B TRP* 3.6 3.2 + - - +
394B ILE* 3.2 28.1 + - - +
402B LEU* 3.3 29.5 - - + +
442B THR* 5.0 0.7 - - + -
446B LEU* 3.9 18.2 - - + -
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 3.3 37.0 - - + +
120B ARG* 4.2 22.0 - - + +
122B TYR* 3.7 12.1 - - + +
387B VAL* 3.2 10.3 + - + +
388B GLY 3.1 8.0 + - - +
390B ALA* 1.3 77.9 - - - +
392B TYR* 1.3 53.4 + - - +
394B ILE* 3.2 3.6 + - - +
395B GLU* 2.7 40.8 + - - +
445B ILE* 4.4 8.5 - - + -
446B LEU* 3.4 27.1 - - + -
449B GLN* 4.0 25.6 - - + -
450B VAL* 4.3 13.5 - - + -
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Residues in contact with TYR 392 (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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122B TYR* 3.5 35.1 + + + -
208B PHE* 3.8 25.8 + + - +
223B LEU* 5.0 2.2 - - + -
224B PRO* 4.8 6.8 - - + +
306B TYR* 2.5 60.3 + + + -
388B GLY 2.8 17.1 + - - +
389B ASN* 3.5 12.6 - - - +
391B LEU* 1.3 75.5 - - - +
393B TRP* 1.3 88.5 + + - +
394B ILE 3.0 0.3 + - - -
396B ARG* 2.6 49.4 + - + +
397B PHE* 3.5 25.3 - + - -
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Residues in contact with TRP 393 (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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289B ILE* 3.4 30.1 - - + -
290B ASN* 4.5 9.5 - - + +
305B LEU 3.2 23.0 + - - -
306B TYR 4.3 0.4 - - - -
307B ALA 4.2 0.7 - - - -
308B PRO* 3.7 26.2 - - + -
318B PHE* 3.8 5.8 - + - -
334B LEU* 3.7 25.1 - - + +
336B TRP* 4.3 13.4 - + - -
389B ASN* 3.0 40.9 + - - +
390B ALA* 4.0 4.7 - - - +
392B TYR* 1.3 91.3 - + - +
394B ILE* 1.3 62.6 + - - +
397B PHE* 3.2 60.1 + + + +
399B ILE* 3.3 20.1 + - + +
402B LEU* 4.5 6.7 - - + -
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Residues in contact with ILE 394 (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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227B VAL 4.4 3.6 - - - +
229B GLN* 5.5 5.4 - - + +
390B ALA 3.2 17.5 + - - +
391B LEU* 3.6 3.1 - - - +
392B TYR 3.1 1.0 - - - -
393B TRP* 1.3 77.9 - - - +
395B GLU* 1.3 59.4 + - + +
398B GLY* 3.0 26.5 + - - -
399B ILE* 3.2 30.5 - - + +
400B ASP 5.3 1.3 - - - +
401B ALA* 5.5 1.1 - - - +
402B LEU* 4.3 15.9 - - + -
446B LEU* 4.4 12.3 - - + -
450B VAL* 3.7 37.9 - - + -
453B ALA* 3.7 25.6 - - + -
454B VAL 5.8 0.9 - - - +
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Residues in contact with GLU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ARG* 2.7 47.6 + - - -
122B TYR* 3.3 13.5 + - - +
123B GLU* 4.6 0.3 - - - +
226B LYS* 3.1 32.3 + - + +
227B VAL 2.6 38.4 + - - +
391B LEU* 2.7 23.0 + - - +
392B TYR 4.3 0.2 - - - +
394B ILE* 1.3 74.9 - - + +
396B ARG* 1.3 56.7 + - + +
397B PHE 3.5 0.2 - - - -
449B GLN 4.6 2.1 - - - +
450B VAL* 3.9 25.8 - - + +
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Residues in contact with ARG 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TYR* 4.1 15.5 + - + -
123B GLU* 3.0 35.0 + - - +
223B LEU* 3.8 19.9 + - + +
224B PRO* 2.9 49.4 + - + +
225B GLU 2.6 29.6 + - - -
226B LYS* 4.0 25.2 - - - +
227B VAL* 4.4 0.9 - - - -
319B ARG* 3.2 14.9 + - - -
392B TYR* 2.6 45.5 + - + +
395B GLU* 1.3 79.6 - - + +
397B PHE* 1.3 62.2 + - + +
398B GLY 3.8 0.2 - - - -
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Residues in contact with PHE 397 (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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224B PRO* 4.0 17.9 - - + -
227B VAL* 3.9 6.6 - - - +
308B PRO* 3.8 16.6 - - + -
315B ARG* 3.4 28.5 - - - -
318B PHE* 3.4 32.3 - + + -
319B ARG* 3.9 26.4 + - + +
322B ILE* 3.0 28.8 - - + +
323B ASP* 4.8 0.5 - - - +
392B TYR* 3.5 30.1 - + - -
393B TRP* 3.2 36.0 + + + +
396B ARG* 1.3 82.6 - - + +
398B GLY* 1.3 60.2 + - - +
399B ILE* 3.2 10.5 + - + -
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Residues in contact with GLY 398 (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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227B VAL* 3.6 26.8 - - - +
229B GLN* 5.5 0.3 + - - -
233B ARG* 4.6 2.5 + - - -
322B ILE* 4.3 0.2 - - - -
326B HIS* 3.0 26.6 + - - -
394B ILE 3.0 15.9 + - - -
397B PHE* 1.3 78.8 - - - +
399B ILE* 1.3 66.8 + - - +
400B ASP* 3.2 6.8 + - - +
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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
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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