Contacts of the helix formed by residues 378 - 391 (chain B) in PDB entry 3RAW
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 378 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B ARG* 3.6 10.5 - - - +
376B THR* 3.3 4.5 + - - -
377B HIS* 1.3 101.1 - - + +
379B ASN* 1.3 71.2 + - - +
380B ARG* 3.0 27.7 + - - +
381B GLU* 3.2 25.7 + - + +
382B HIS* 3.0 21.1 + - - +
406B TYR* 4.6 4.7 - - - -
414B TRP* 4.3 5.2 - - - -
420B ASP* 4.6 4.3 - - - +
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Residues in contact with ASN 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ILE* 6.1 3.0 - - - +
338B ARG* 2.9 22.6 + - - +
341B ARG* 4.4 4.5 + - - +
346B ILE* 3.6 36.3 + - + +
378B GLU* 1.3 76.1 + - - +
380B ARG* 1.3 61.3 + - - +
382B HIS* 3.2 7.2 + - - +
383B LEU* 2.9 34.6 + - - +
403B LYS* 6.2 0.6 - - - +
406B TYR* 3.1 32.3 + - + +
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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
----------------------------------------------------------
378B GLU* 3.0 19.2 + - - +
379B ASN* 1.3 76.6 - - - +
381B GLU* 1.3 64.5 + - - +
383B LEU* 3.2 7.5 + - - +
384B VAL* 2.9 24.1 + - + +
405B LYS* 3.1 30.9 + - - +
406B TYR* 3.5 36.6 - - + +
412B LEU* 5.1 2.7 - - + -
413B VAL* 3.0 57.4 + - - +
414B TRP* 3.5 22.4 - - + +
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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
----------------------------------------------------------
400A ARG* 2.9 37.8 + - - -
376B THR* 2.6 21.1 + - - +
377B HIS* 3.1 20.7 + - - -
378B GLU* 3.2 14.9 + - + +
379B ASN 3.4 0.2 - - - -
380B ARG* 1.3 79.1 - - - +
382B HIS* 1.3 56.6 + - - +
384B VAL* 3.1 3.7 + - - +
385B MET* 2.8 41.9 + - + +
414B TRP* 3.6 24.5 - - + -
420B ASP* 3.3 17.1 - - - +
424B VAL* 3.8 18.8 - - + +
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Residues in contact with HIS 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ARG* 3.1 35.2 + - + +
339B HIS 4.5 0.2 - - - -
341B ARG* 3.4 20.1 + - + +
346B ILE* 3.5 17.8 - - + +
374B PHE* 3.5 33.1 - + + +
376B THR* 3.5 27.0 + - + +
378B GLU 3.0 16.3 + - - +
379B ASN* 3.2 12.2 + - - +
381B GLU* 1.3 74.8 - - - +
383B LEU* 1.3 58.8 + - - +
385B MET* 3.0 5.6 + - - +
386B MET* 2.9 43.0 + - + +
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B PRO* 4.8 4.5 - - + -
346B ILE* 4.1 17.7 - - + -
347B LEU* 3.9 27.6 - - + -
379B ASN 2.9 20.0 + - - +
380B ARG* 3.6 6.5 - - - +
382B HIS* 1.3 75.4 - - - +
384B VAL* 1.3 62.8 + - - +
386B MET* 3.3 21.7 + - - +
387B GLU* 3.1 20.1 + - - +
393B ILE* 3.9 19.3 - - + +
406B TYR* 3.8 34.5 - - + -
407B PHE* 4.6 0.9 - - + -
412B LEU* 3.6 29.7 - - + +
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Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ARG* 2.9 19.7 + - + +
381B GLU* 3.6 7.2 - - - +
383B LEU* 1.3 76.4 - - - +
385B MET* 1.3 60.7 + - - +
387B GLU* 3.2 4.1 + - + +
388B LYS* 3.0 33.9 + - + +
412B LEU* 3.8 21.3 - - + -
414B TRP* 3.5 55.4 - - + +
424B VAL* 4.0 16.6 - - + -
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Residues in contact with MET 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B PHE* 3.9 20.6 - - + -
375B GLN 3.7 23.6 - - - +
376B THR* 3.7 22.9 - - - -
381B GLU* 2.8 31.9 + - + +
382B HIS* 3.4 5.2 - - - +
384B VAL* 1.3 73.1 - - - +
386B MET* 1.3 59.1 + - - +
388B LYS* 3.3 5.8 + - - +
389B ILE* 2.9 35.3 + - + +
423B TYR* 3.6 31.9 - - + -
424B VAL* 3.7 26.9 - - + -
428B CYS* 3.9 19.3 - - - -
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Residues in contact with MET 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ARG 3.7 11.7 - - - +
343B PRO* 3.7 29.8 - - - -
346B ILE* 3.6 22.4 - - + -
358B TRP* 3.8 13.5 - - + -
374B PHE* 3.9 23.1 - - + -
382B HIS* 2.9 42.5 + - + +
383B LEU* 3.5 16.6 - - - +
384B VAL 3.3 0.2 - - - -
385B MET* 1.3 76.8 - - - +
387B GLU* 1.3 58.0 + - - +
390B LEU* 2.8 36.3 + - + +
391B GLY 3.5 0.3 + - - -
455B PHE* 3.6 23.0 - - + -
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Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B LEU 3.1 17.8 + - - +
384B VAL* 3.2 6.9 + - + +
386B MET* 1.3 76.0 - - - +
388B LYS* 1.3 60.5 + - + +
391B GLY* 2.9 38.6 + - - +
392B PRO* 3.7 9.1 - - - +
393B ILE* 3.2 36.2 + - + +
398B ILE* 5.3 3.6 - - - +
411B GLY* 5.8 1.0 - - - -
412B LEU* 3.6 34.3 + - + +
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Residues in contact with LYS 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B VAL* 3.0 35.4 + - + +
385B MET 3.7 4.0 - - - +
387B GLU* 1.3 77.4 - - + +
389B ILE* 1.3 61.6 + - - +
414B TRP* 5.8 1.3 - - - +
416B GLU* 3.8 18.6 + - - +
424B VAL* 3.9 21.8 - - + +
425B LYS* 3.4 33.5 - - + +
428B CYS* 3.8 24.9 - - + +
429B LYS* 3.7 0.9 - - - -
430B PRO* 3.5 23.7 - - - +
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Residues in contact with ILE 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B LEU* 3.8 32.8 - - + +
374B PHE* 3.6 22.2 - - + -
385B MET 2.9 21.0 + - - +
388B LYS* 1.3 80.0 - - - +
390B LEU* 1.3 77.2 + - + +
428B CYS* 4.0 24.7 - - + -
429B LYS 3.6 20.6 - - - +
430B PRO* 3.6 4.2 - - - +
431B LEU* 3.0 46.2 + - + +
434B TYR* 4.7 4.7 - - + +
450B ARG* 5.1 2.4 + - - -
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B TRP* 3.5 32.5 - - + -
374B PHE* 4.2 13.2 - - + -
386B MET* 2.8 15.8 + - - +
389B ILE* 1.3 96.1 - - + +
391B GLY* 1.3 59.8 + - - +
392B PRO 5.3 0.2 - - - +
431B LEU* 4.0 20.4 - - + -
450B ARG* 4.7 17.7 + - + +
453B LEU* 3.7 34.1 - - + +
455B PHE* 4.0 17.0 - - + -
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Residues in contact with GLY 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B GLU* 2.9 29.3 + - - -
388B LYS 4.7 0.2 - - - -
389B ILE 3.7 0.6 - - - -
390B LEU* 1.3 79.5 - - - +
392B PRO* 1.3 80.0 - - - +
455B PHE* 3.1 13.4 - - - -
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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