Contacts of the helix formed by residues 372 - 391 (chain B) in PDB entry 6FEQ
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 SER 372 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B THR* 5.3 4.2 - - - +
371B THR* 1.3 80.1 - - - +
373B PHE* 1.3 64.0 + - - +
374B CYS* 4.2 4.0 + - - +
375B HIS* 3.3 23.4 + - - +
376B GLN* 3.3 20.7 + - - +
465B ARG* 6.4 0.2 - - - -
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Residues in contact with PHE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B SER* 1.3 73.1 - - - +
374B CYS* 1.3 77.1 + - - +
376B GLN* 3.3 8.8 + - - +
377B LEU* 3.2 39.0 + - + +
465B ARG* 4.7 28.1 - - - +
467B SER* 3.6 26.9 - - - -
468B SER* 3.8 25.1 - - - -
471B LEU* 4.1 19.3 - - + -
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Residues in contact with CYS 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B SER* 4.2 3.4 + - - +
373B PHE* 1.3 90.3 - - - +
375B HIS* 1.3 62.8 + - - +
377B LEU* 3.5 6.2 + - - +
378B ARG* 3.3 28.5 + - - +
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Residues in contact with HIS 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ALA* 3.6 19.3 + - - +
146B LEU* 4.7 2.0 - - + -
150B THR* 4.8 12.8 - - + +
157B LYS* 5.6 3.8 + - - -
371B THR* 3.5 23.8 - - + -
372B SER* 3.3 22.3 + - - +
373B PHE 3.2 0.8 - - - -
374B CYS* 1.3 77.6 - - - +
376B GLN* 1.3 64.7 + - - +
378B ARG* 3.4 23.4 + - - +
379B TRP* 3.1 55.3 + + - -
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Residues in contact with GLN 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 4.1 22.0 - - + -
369B TYR* 4.6 11.5 - - - +
371B THR* 3.3 31.7 + - - +
372B SER 3.3 13.6 + - - +
373B PHE* 3.3 8.7 + - - +
374B CYS 3.3 0.6 - - - -
375B HIS* 1.3 78.8 - - - +
377B LEU* 1.3 57.4 + - - +
378B ARG 3.3 0.2 + - - -
379B TRP* 3.4 1.6 + - - +
380B VAL* 3.0 34.5 + - - +
463B TYR 3.8 5.8 + - - +
464B TYR* 3.6 24.8 - - + +
465B ARG* 3.2 14.7 + - - +
468B SER* 3.0 30.2 + - - +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B PHE* 3.2 36.4 + - + +
374B CYS* 3.5 6.7 + - - +
375B HIS 3.3 0.2 - - - -
376B GLN* 1.3 76.2 - - - +
378B ARG* 1.3 67.4 + - - +
380B VAL* 4.7 1.3 - - - +
381B SER* 3.3 18.2 + - - -
468B SER* 4.5 13.4 - - - +
471B LEU* 3.7 31.6 - - + +
472B GLY* 4.2 14.5 - - - +
475B LEU* 4.1 25.8 - - + -
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Residues in contact with ARG 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B CYS* 3.3 18.4 + - - +
375B HIS* 3.4 41.3 + - - +
376B GLN 3.2 0.4 - - - -
377B LEU* 1.3 77.4 - - - +
379B TRP* 1.3 68.7 + - + +
381B SER* 3.1 4.8 + - - -
382B LYS* 2.7 44.3 + - + +
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Residues in contact with TRP 379 (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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141B GLN* 5.1 18.4 - - + -
142B PHE* 3.4 33.3 - + + -
145B ALA* 4.0 24.2 - - + -
146B LEU* 4.6 10.1 - - + -
375B HIS* 3.1 57.7 + + - +
376B GLN 3.4 3.8 + - - +
378B ARG* 1.3 89.0 - - + +
380B VAL* 1.3 63.7 + - - +
382B LYS* 3.9 40.3 - - + +
383B ARG* 3.1 16.8 + - - +
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Residues in contact with VAL 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B PHE* 4.5 7.9 - - + -
146B LEU* 4.7 8.3 - - + -
376B GLN 3.0 20.5 + - - +
377B LEU* 4.6 1.8 - - - +
379B TRP* 1.3 77.3 - - - +
381B SER* 1.3 61.7 + - - +
383B ARG* 3.4 12.7 + - - +
384B SER* 3.2 23.9 + - - -
464B TYR* 4.1 33.7 - - + -
468B SER 4.5 9.4 - - - +
469B TYR* 4.4 32.8 - - + +
472B GLY* 4.6 1.3 - - - -
473B LYS* 4.6 12.1 - - + +
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Residues in contact with SER 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LEU 3.3 18.4 + - - -
378B ARG* 3.1 3.4 + - - -
380B VAL* 1.3 79.5 - - - +
382B LYS* 1.3 61.7 + - - +
385B PHE* 3.2 24.4 + - - +
472B GLY* 3.8 18.5 + - - -
475B LEU* 4.2 15.6 + - - +
476B SER* 3.3 24.7 + - - -
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Residues in contact with LYS 382 (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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378B ARG* 2.7 28.9 + - + +
379B TRP* 3.9 45.4 - - + +
381B SER* 1.3 72.5 - - - +
383B ARG* 1.3 65.2 + - - +
385B PHE* 3.5 6.1 + - - +
386B LYS* 3.3 47.8 + - - +
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Residues in contact with ARG 383 (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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131B MET* 2.8 61.6 - - + +
134B LEU* 4.2 17.0 - - + +
139B ASN* 5.5 0.7 - - - -
142B PHE* 3.2 50.8 - - + -
379B TRP* 3.1 17.9 + - - +
380B VAL* 3.9 13.6 + - - +
381B SER 3.4 0.2 - - - -
382B LYS* 1.3 77.2 - - - +
384B SER* 1.3 65.3 + - - +
386B LYS* 3.4 9.4 + - - +
387B ASN* 3.1 18.5 + - - +
451B GLU* 4.6 4.0 + - - -
454B LEU* 3.8 18.2 - - - +
458B GLU* 4.5 7.9 + - - -
464B TYR* 5.3 1.4 + - - -
469B TYR* 4.7 14.8 - - - -
473B LYS* 4.9 11.5 - - - +
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Residues in contact with SER 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B VAL* 3.2 15.2 + - - -
383B ARG* 1.3 82.8 - - - +
385B PHE* 1.3 59.3 + - - +
387B ASN* 3.2 13.2 + - - +
388B LEU 2.9 21.3 + - - -
473B LYS* 3.5 22.6 + - - +
476B SER* 3.2 14.0 + - - -
477B ASP* 2.8 35.5 + - - +
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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
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381B SER* 3.2 18.8 + - - +
382B LYS* 3.8 6.5 - - - +
383B ARG 3.2 0.4 - - - -
384B SER* 1.3 75.4 - - - +
386B LYS* 1.3 66.6 + - + +
388B LEU* 3.0 16.5 + - + +
389B LEU* 3.0 56.4 + - + +
476B SER* 3.0 25.7 + - - +
480B PRO* 5.3 8.1 - - + -
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Residues in contact with LYS 386 (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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133B THR* 4.5 1.6 - - - +
134B LEU* 4.4 17.0 - - + -
138B GLU* 3.9 35.3 + - - +
382B LYS* 3.3 40.5 + - - +
383B ARG* 3.7 8.1 - - - +
384B SER 3.4 0.2 - - - -
385B PHE* 1.3 80.8 - - + +
387B ASN* 1.3 54.4 + - - +
389B LEU* 4.1 6.9 - - + +
390B GLY* 2.6 34.8 + - - -
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Residues in contact with ASN 387 (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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131B MET* 3.4 31.2 - - + +
133B THR* 3.3 21.7 - - - +
134B LEU* 4.5 0.8 - - - +
383B ARG 3.1 14.0 + - - +
384B SER* 3.3 16.7 + - - +
385B PHE 3.2 0.4 - - - -
386B LYS* 1.3 77.2 - - - +
388B LEU* 1.3 59.9 + - - +
391B ASN* 3.4 24.8 + - - +
451B GLU* 3.9 17.4 + - - +
473B LYS* 5.4 3.4 - - - +
477B ASP* 5.8 1.0 + - - -
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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
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384B SER 2.9 13.2 + - - +
385B PHE* 3.0 19.5 + - + +
387B ASN* 1.3 78.5 - - - +
389B LEU* 1.3 65.4 + - + +
391B ASN* 3.2 19.9 - - - +
392B PRO* 5.0 0.5 - - - +
395B SER* 4.0 22.5 + - - +
476B SER 3.8 20.4 - - - +
477B ASP* 4.0 14.4 - - + +
480B PRO* 4.2 4.7 - - + -
481B MET* 3.7 45.3 - - + -
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Residues in contact with LEU 389 (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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385B PHE* 3.0 49.9 + - + +
386B LYS* 4.1 6.3 - - + +
388B LEU* 1.3 81.5 - - + +
390B GLY* 1.3 63.2 + - - +
391B ASN 3.2 1.7 + - - -
392B PRO* 3.8 16.2 - - - +
396B ILE* 6.3 3.1 - - + -
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Residues in contact with GLY 390 (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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133B THR* 2.9 31.0 + - - -
177B LYS* 5.4 6.4 + - - -
183B ILE* 3.5 17.2 - - - +
386B LYS 2.6 21.4 + - - -
387B ASN 4.1 0.9 - - - -
389B LEU* 1.3 72.9 - - - +
391B ASN* 1.3 54.9 + - - +
392B PRO* 3.3 9.1 - - - +
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Residues in contact with ASN 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B THR* 5.1 3.4 - - - +
180B THR* 5.2 12.8 - - - +
182B PHE* 4.0 24.1 - - - +
387B ASN* 3.4 21.1 + - - +
388B LEU* 3.2 14.2 - - - +
389B LEU 3.2 0.8 - - - -
390B GLY* 1.3 76.4 - - - +
392B PRO* 1.3 68.8 - - - +
393B GLN 3.9 9.3 - - - +
394B ALA* 4.0 20.5 - - + +
395B SER* 3.8 10.9 + - - -
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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
------------------------------------------------------------
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