Contacts of the helix formed by residues 356 - 373 (chain B) in PDB entry 2F61
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 356 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TYR* 4.3 1.3 - - - +
12B SER* 3.9 2.7 - - - -
353B ARG* 3.1 27.6 + - - -
354B LEU 3.4 1.0 + - - -
355B GLY* 1.3 73.5 - - - +
357B TRP* 1.3 60.6 + - - +
359B ARG* 3.1 37.7 + - - +
360B GLY 3.7 6.8 + - - -
414B GLN* 4.2 1.4 + - - -
415B PRO* 3.3 17.6 - - - +
416B MET* 5.0 1.2 + - - +
1503B SO4 2.7 31.7 + - - -
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Residues in contact with TRP 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B SER* 2.8 20.2 + - - +
13B SER* 3.8 7.4 - - - -
42B SER* 3.6 24.9 - - - -
43B THR 3.4 24.2 - - - -
44B ARG* 3.3 36.6 - - + -
48B ARG* 3.6 13.0 - - - -
355B GLY 3.0 2.4 + - - -
356B SER* 1.3 71.9 - - - +
358B ASP* 1.3 63.9 + - - +
359B ARG 3.3 0.2 - - - -
360B GLY* 3.3 1.7 + - - -
361B MET* 3.2 51.0 + - + +
415B PRO* 3.8 18.8 - - + -
418B TYR* 6.2 1.1 - - + -
419B HIS* 3.3 32.8 - + - -
487B TYR* 3.4 36.3 + + + -
488B SER* 4.0 3.1 - - - -
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Residues in contact with ASP 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B SER* 4.0 2.5 - - - +
357B TRP* 1.3 80.3 - - - +
359B ARG* 1.3 64.6 + - + +
361B MET* 3.3 26.2 + - + +
362B GLN* 3.2 39.3 + - - +
1503B SO4 3.0 26.1 + - - +
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Residues in contact with ARG 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ASP* 5.4 2.3 + - - +
343B VAL* 3.6 30.7 - - + +
344B GLY* 3.8 10.4 - - - +
349B GLU* 3.3 18.8 - - - +
350B GLN 2.7 24.6 + - - -
351B SER 3.0 17.3 + - - -
353B ARG* 3.1 40.0 - - - +
356B SER* 3.1 25.5 + - - +
358B ASP* 1.3 77.1 - - + +
360B GLY* 1.3 65.2 + - - +
362B GLN* 3.3 13.7 + - + +
363B TYR* 3.3 25.6 + - - -
399B ASP* 2.7 35.1 + - - +
416B MET* 3.9 10.5 - - + -
1503B SO4 5.3 0.2 + - - -
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Residues in contact with GLY 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B SER 3.7 4.9 + - - -
357B TRP 3.3 4.5 + - - -
358B ASP 3.2 0.8 - - - -
359B ARG* 1.3 79.2 - - - +
361B MET* 1.3 56.0 + - - +
363B TYR* 2.9 20.8 + - - +
364B SER 3.0 11.3 + - - -
415B PRO* 4.1 1.8 - - - -
416B MET* 3.9 20.1 - - - +
419B HIS* 3.3 30.8 - - - -
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Residues in contact with MET 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B TRP* 3.2 43.6 + - + +
358B ASP* 3.3 36.3 + - + +
360B GLY* 1.3 74.8 - - - +
362B GLN* 1.3 57.2 + - + +
364B SER* 3.2 10.3 + - - -
365B HIS* 2.8 34.0 + - - +
419B HIS* 3.8 8.6 - - + -
461B LEU* 4.0 4.8 - - + +
462B ASN 4.5 2.9 - - - +
463B ARG* 4.1 35.4 - - + +
487B TYR* 3.8 27.8 - - + -
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Residues in contact with GLN 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LEU* 2.5 50.5 + - + +
315B ASP* 4.0 10.4 - - - +
317B LEU* 5.8 5.3 - - - +
343B VAL* 4.1 4.7 - - + +
358B ASP* 3.2 27.8 + - - +
359B ARG* 3.4 15.7 - - + +
360B GLY 3.1 0.6 - - - -
361B MET* 1.3 77.3 - - + +
363B TYR* 1.3 57.7 - - - +
365B HIS* 3.8 5.3 + - - +
366B SER* 2.9 30.3 + - - -
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Residues in contact with TYR 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LEU* 3.3 26.5 - - + -
341B ALA 3.7 8.3 + - - -
342B CYS* 4.0 6.4 - - - +
343B VAL* 4.1 9.1 + - + +
359B ARG 3.3 13.6 + - - +
360B GLY* 2.9 10.6 + - - +
362B GLN* 1.3 76.0 - - - +
364B SER* 1.3 67.4 + - - +
366B SER* 2.9 4.8 + - - -
367B ILE* 2.9 31.1 + - + +
378B TRP* 3.4 30.3 - + - -
380B ASP* 2.5 37.4 + - - -
399B ASP 5.2 3.6 + - - -
401B PRO* 4.3 8.2 - - + +
416B MET* 3.4 35.8 - - + +
419B HIS* 4.5 8.1 - - + -
420B LEU* 3.7 18.6 - - + +
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Residues in contact with SER 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B GLY 3.0 1.2 + - - -
361B MET* 3.2 6.2 + - - -
363B TYR* 1.3 77.5 - - - +
365B HIS* 1.3 59.0 + - - +
367B ILE* 4.5 1.8 - - - +
368B ILE* 2.9 35.5 + - - +
419B HIS* 2.9 32.5 + - - +
423B PHE* 3.6 29.0 - - - -
461B LEU* 3.2 25.6 - - - +
489B ILE* 4.5 4.0 - - - -
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Residues in contact with HIS 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LEU* 5.7 9.4 - - + -
361B MET 2.8 21.8 + - - +
362B GLN* 3.9 5.5 + - - +
364B SER* 1.3 77.0 + - - +
366B SER* 1.3 57.3 + - - +
368B ILE* 3.9 4.8 - - - +
369B THR* 2.7 57.1 + - + -
445B ASP* 3.2 19.3 + - - -
461B LEU* 3.9 11.9 - - + -
463B ARG* 3.0 47.2 + - - -
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Residues in contact with SER 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B TRP* 3.7 13.7 - - - -
314B LEU* 3.2 27.6 - - - +
362B GLN 2.9 20.3 + - - -
363B TYR 3.4 4.3 - - - -
365B HIS* 1.3 78.8 + - - +
367B ILE* 1.3 57.0 + - - +
369B THR* 3.2 5.3 + - - -
370B ASN* 2.6 48.4 + - - -
378B TRP* 3.8 11.6 + - - -
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Residues in contact with ILE 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE* 3.9 18.2 - - + -
363B TYR 2.9 23.3 + - - +
364B SER 3.8 3.6 - - - +
366B SER* 1.3 77.2 - - - +
368B ILE* 1.3 56.4 + - - +
370B ASN* 3.2 1.2 + - - +
371B LEU* 2.9 34.2 + - + +
378B TRP* 3.4 37.9 - - + +
420B LEU* 3.4 38.1 - - + -
423B PHE* 3.6 41.7 - - + -
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Residues in contact with ILE 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B SER 2.9 22.0 + - - +
365B HIS* 3.9 4.9 - - - +
367B ILE* 1.3 76.7 - - - +
369B THR* 1.3 65.6 + - - +
371B LEU* 3.3 5.4 + - - +
372B LEU* 3.0 42.8 + - + +
423B PHE* 3.4 25.4 - - + -
445B ASP* 3.8 39.9 - - + +
446B ALA* 4.0 20.4 - - - +
447B VAL* 4.3 7.8 - - + +
459B VAL* 4.6 6.1 - - + +
461B LEU* 3.9 17.0 - - + +
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Residues in contact with THR 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B TRP* 4.5 15.3 - - + -
320B ALA* 3.9 25.8 - - + -
324B LEU* 5.8 0.2 - - + -
365B HIS* 2.7 43.9 + - + -
366B SER* 3.5 7.4 - - - -
368B ILE* 1.3 80.7 - - - +
370B ASN* 1.3 61.7 + - - +
372B LEU* 3.5 6.2 + - - -
373B TYR* 3.2 28.2 + - + +
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Residues in contact with ASN 370 (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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310B VAL* 4.7 0.9 - - - +
312B TRP* 2.7 49.4 + - - +
324B LEU* 4.0 3.0 - - - +
338B ALA* 4.1 2.3 - - - +
366B SER* 2.6 40.5 + - - +
367B ILE 3.6 4.3 - - - +
368B ILE 3.1 0.4 - - - -
369B THR* 1.3 72.9 - - - +
371B LEU* 1.3 62.6 + - + +
373B TYR 2.9 16.8 + - - -
375B VAL* 3.2 52.9 + - + +
378B TRP* 3.6 17.2 - - + +
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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
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76B GLN* 2.7 27.9 + - - +
78B VAL* 4.6 13.9 - - + -
81B PHE* 4.5 20.6 - - + -
367B ILE* 2.9 36.9 + - + +
368B ILE 3.9 3.8 - - - +
370B ASN* 1.3 73.6 - - + +
372B LEU* 1.3 60.6 + - - +
375B VAL* 3.6 18.6 - - + +
376B VAL 5.2 4.0 - - - -
377B GLY* 5.4 1.8 - - - +
378B TRP* 6.4 0.4 - - + -
423B PHE* 4.3 9.0 - - + -
427B ILE* 5.5 1.8 - - + -
433B ARG* 3.1 17.0 - - + -
447B VAL* 4.0 31.4 - - + -
449B LEU* 4.3 16.8 - - + -
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Residues in contact with LEU 372 (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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368B ILE* 3.0 38.2 + - + +
369B THR* 3.8 8.5 - - - +
370B ASN 3.1 0.2 - - - -
371B LEU* 1.3 76.9 - - - +
373B TYR* 1.3 74.7 + - + +
374B HIS* 3.5 4.5 + - - -
433B ARG* 3.3 45.9 + - - +
445B ASP* 6.2 0.2 - - - +
446B ALA 4.0 17.7 - - - +
447B VAL* 4.2 10.1 - - + -
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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
----------------------------------------------------------
320B ALA* 3.9 22.4 - - + -
321B LYS* 3.4 47.8 + - + +
324B LEU* 4.0 16.7 - - + +
325B GLY* 4.2 11.2 - - - -
336B LEU* 3.8 11.6 - - - +
369B THR* 3.2 22.4 - - + +
370B ASN 2.9 6.0 + - - +
372B LEU* 1.3 93.5 - - + +
374B HIS* 1.3 77.0 + + + +
375B VAL* 3.1 11.7 + - - +
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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) + - + + + + + -
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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