Contacts of the helix formed by residues 411 - 427 (chain B) in PDB entry 5B2R
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 PRO 411 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B GLY* 4.3 0.2 - - - -
167B HIS* 3.6 27.6 - - + +
170B ILE* 3.9 20.9 - - + -
174B LEU* 4.2 9.0 - - + -
301B LEU* 6.2 0.7 - - + -
302B LEU* 6.1 2.2 - - + -
305B ILE* 3.6 19.3 - - + -
409B SER 3.3 6.7 - - - +
410B ILE* 1.3 91.9 - - - +
412B HIS* 1.3 65.9 + - - +
413B GLN* 3.4 16.8 - - - +
414B ILE* 3.0 29.9 + - + +
415B HIS* 3.8 1.4 + - - -
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Residues in contact with HIS 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ARG 3.0 27.1 - - - +
166B GLY 3.6 5.4 - - - +
167B HIS 2.8 33.5 + - - +
168B PHE* 3.3 44.6 - + + -
170B ILE 4.8 1.4 + - - -
411B PRO* 1.3 71.2 - - - +
413B GLN* 1.3 95.0 + - + +
414B ILE 3.1 0.2 + - - -
415B HIS* 3.2 3.4 + - - +
416B LEU* 2.8 33.2 + - + +
444B LEU* 4.0 14.9 - - + +
445B THR* 4.4 17.2 - - + +
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Residues in contact with GLN 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B HIS 4.2 0.7 - - - +
170B ILE* 2.8 36.9 + - - +
172B GLY 2.8 25.2 + - - +
173B ASP* 4.7 1.8 - - - +
174B LEU* 3.8 42.9 - - + +
176B PRO* 6.0 1.7 - - - +
411B PRO* 3.1 16.0 - - - +
412B HIS* 1.3 102.1 + - + +
414B ILE* 1.3 58.1 + - - +
416B LEU* 3.6 15.2 - - + +
417B GLY* 2.9 25.1 + - - -
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Residues in contact with ILE 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 4.9 7.0 - - + -
176B PRO* 4.1 17.7 - - + -
302B LEU* 3.7 30.3 - - + -
305B ILE* 4.1 5.2 - - + -
306B LEU* 4.1 16.4 - - + -
316B PRO* 5.8 1.6 - - + -
317B LEU* 3.5 37.7 - - + +
410B ILE* 4.1 5.6 - - + -
411B PRO* 3.0 34.6 + - + +
413B GLN* 1.3 74.2 - - - +
415B HIS* 1.3 66.9 + - - +
417B GLY* 3.3 9.8 + - - -
418B GLU* 3.4 15.5 + - + +
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Residues in contact with HIS 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A G 4.8 1.6 + - - -
136B TYR* 5.4 4.7 - + - -
139B ARG* 2.9 37.6 + - - +
160B HIS* 6.1 0.2 - + - -
161B MET* 3.9 9.5 - - + +
164B PHE 3.4 17.3 + - - -
165B ARG 3.4 32.8 - - - +
166B GLY* 3.6 8.4 + - - -
317B LEU* 3.4 23.6 - - + +
410B ILE* 3.7 22.5 - - + +
411B PRO 3.8 2.1 + - - -
412B HIS 3.2 5.5 + - - +
414B ILE* 1.3 76.6 - - - +
416B LEU* 1.3 62.9 + - - +
418B GLU* 3.2 4.7 + - - +
419B LEU* 2.9 22.5 + - - +
444B LEU* 4.3 12.3 - - + -
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Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASP* 6.1 0.7 - - - +
412B HIS* 2.8 26.4 + - + +
413B GLN* 3.6 16.4 - - + +
414B ILE 3.2 0.2 - - - -
415B HIS* 1.3 73.0 - - - +
417B GLY* 1.3 56.3 + - - +
419B LEU* 3.2 11.3 + - + -
420B HIS* 2.8 32.0 + - + +
441B GLU* 4.2 27.4 - - + +
444B LEU* 4.1 16.0 - - + +
445B THR* 3.8 31.0 - - + -
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Residues in contact with GLY 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B PRO* 6.4 2.0 - - - -
314B LYS 4.9 4.6 - - - +
413B GLN 2.9 15.1 + - - -
414B ILE 3.3 4.0 + - - -
415B HIS 3.3 0.6 - - - -
416B LEU* 1.3 77.9 - - - +
418B GLU* 1.3 57.9 + - - +
420B HIS* 3.6 6.6 + - - +
421B ALA* 3.0 27.9 + - - +
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Residues in contact with GLU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ARG* 3.0 26.1 + - - +
143B VAL* 3.6 11.3 - - + +
161B MET* 3.5 14.4 - - + +
314B LYS 4.3 2.7 - - - +
315B ALA* 3.3 32.7 - - + +
316B PRO* 5.6 1.1 - - + -
317B LEU* 3.6 9.2 + - + +
318B SER* 2.8 46.5 + - - -
414B ILE* 3.4 10.4 + - + +
415B HIS 3.2 6.1 + - - +
417B GLY* 1.3 72.2 - - - +
419B LEU* 1.3 65.5 + - - +
421B ALA* 3.3 0.8 + - - -
422B ILE* 3.0 28.4 + - - +
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU* 3.6 46.4 - - + +
161B MET* 3.3 17.8 - - - -
162B ILE* 4.1 17.5 - - + -
415B HIS 2.9 11.8 + - - +
416B LEU* 3.6 13.5 - - + +
418B GLU* 1.3 76.0 - - - +
420B HIS* 1.3 62.9 + - - +
422B ILE* 3.2 4.2 + - - +
423B LEU* 3.0 34.0 + - + +
440B ILE* 4.1 7.4 - - + +
441B GLU* 3.8 38.6 - - + -
444B LEU* 4.1 12.6 - - + -
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Residues in contact with HIS 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LEU* 2.8 24.0 + - + +
417B GLY* 3.8 7.0 - - - +
419B LEU* 1.3 74.0 - - - +
421B ALA* 1.3 59.8 + - + +
423B LEU* 3.3 6.3 + - - +
424B ARG* 2.9 65.4 + - + +
437B ARG* 3.5 12.7 - - - -
441B GLU* 2.5 41.0 + - - +
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Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B VAL* 3.8 30.3 - - + +
314B LYS* 4.8 9.4 - - + +
417B GLY 3.0 18.9 + - - +
418B GLU* 3.7 4.7 - - - +
419B LEU 3.2 0.2 - - - -
420B HIS* 1.3 81.0 - - + +
422B ILE* 1.3 62.0 + - - +
424B ARG* 3.2 6.9 + - - +
425B ARG* 2.9 29.6 + - - +
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Residues in contact with ILE 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ARG 4.0 6.5 - - - +
142B LEU* 3.6 41.5 - - + +
143B VAL* 3.7 12.1 - - + -
154B ILE* 4.3 19.5 - - + -
157B ALA* 3.8 16.2 - - + -
158B LEU* 4.0 15.0 - - + -
161B MET* 3.6 30.3 - - + -
418B GLU 3.0 15.8 + - - +
419B LEU 3.8 3.8 - - - +
421B ALA* 1.3 74.1 - - - +
423B LEU* 1.3 64.0 + - - +
425B ARG* 3.2 2.9 + - - +
426B GLN* 2.9 28.3 + - + +
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Residues in contact with LEU 423 (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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154B ILE* 5.8 0.4 - - + -
158B LEU* 3.8 29.2 - - + -
419B LEU* 3.0 38.3 + - + +
420B HIS 3.6 5.8 - - - +
421B ALA 3.3 0.2 - - - -
422B ILE* 1.3 76.4 - - + +
424B ARG* 1.3 57.2 + - - +
426B GLN* 4.6 1.8 - - - +
427B GLU* 2.8 39.4 + - - +
433B LEU* 4.4 20.4 - - + +
437B ARG* 3.8 42.2 - - + +
440B ILE* 3.9 22.4 - - + -
441B GLU* 3.9 5.6 - - + +
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Residues in contact with ARG 424 (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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420B HIS* 2.9 49.3 + - + +
421B ALA* 3.6 7.6 - - - +
423B LEU* 1.3 78.0 - - - +
425B ARG* 1.3 65.6 + - + +
427B GLU* 2.8 39.6 + - - +
428B ASP* 3.7 10.6 - - - +
437B ARG* 3.6 38.6 - - - +
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Residues in contact with ARG 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU 3.6 13.7 - - - +
143B VAL 3.1 23.9 + - - +
144B ASP* 3.2 24.6 + - - +
145B SER 3.4 16.7 + - - +
146B THR* 3.4 27.9 - - - +
421B ALA 2.9 17.9 + - - +
422B ILE 3.2 6.9 + - - +
424B ARG* 1.3 79.9 - - + +
426B GLN* 1.3 69.6 + - - +
428B ASP* 3.7 18.5 + - - +
429B PHE* 3.9 10.7 - - - -
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Residues in contact with GLN 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 4.9 8.2 + - + +
145B SER* 4.8 3.8 + - - -
146B THR 5.2 0.6 - - - -
147B ASP 2.8 27.0 + - - -
148B LYS* 3.7 4.2 - - - -
149B ALA* 2.9 33.5 + - + +
154B ILE* 3.5 34.1 - - + +
422B ILE* 2.9 23.9 + - + +
425B ARG* 1.3 86.0 + - + +
427B GLU* 1.3 63.3 + - - +
428B ASP 3.0 5.2 - - - -
429B PHE* 3.0 17.2 + - - -
430B TYR* 3.2 22.5 + - - +
433B LEU* 3.9 10.5 - - + -
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Residues in contact with GLU 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LEU 2.8 20.3 + - - +
424B ARG* 2.8 44.0 + - - +
426B GLN* 1.3 76.0 - - - +
428B ASP* 1.3 70.6 + - - +
429B PHE 3.2 1.1 + - - -
430B TYR 3.5 20.9 + - - +
431B PRO* 4.5 0.5 - - - +
433B LEU* 4.0 7.3 - - + +
434B LYS* 3.6 60.2 + - - +
437B ARG* 3.6 21.3 + - - +
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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