Contacts of the helix formed by residues 403 - 421 (chain B) in PDB entry 3HB1
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 GLY 403 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B GLY 3.0 13.4 + - - -
400B GLY 4.5 2.6 + - - -
401B LEU 3.5 2.6 - - - +
402B ILE* 1.3 79.2 - - - +
404B THR* 1.3 60.1 + - - -
405B PRO* 3.5 7.0 - - - -
407B ARG* 2.8 31.7 + - - +
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Residues in contact with THR 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B GLY 5.1 0.2 - - - -
403B GLY* 1.3 68.0 - - - -
405B PRO* 1.3 77.5 - - + +
407B ARG* 3.4 8.1 + - - +
408B GLU* 3.1 31.9 + - + +
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Residues in contact with PRO 405 (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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402B ILE 5.3 0.7 - - - +
403B GLY* 3.6 4.3 - - - -
404B THR* 1.3 99.6 - - + +
406B LYS* 1.3 71.2 + - + +
408B GLU* 3.4 5.7 + - + +
409B THR* 3.3 27.4 + - - +
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Residues in contact with LYS 406 (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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311B MET* 3.4 12.8 - - + +
314B ASN* 3.3 34.8 + - + +
318B THR* 5.1 7.7 + - - +
319B HIS* 6.1 2.8 - - + -
402B ILE* 3.3 39.3 - - + +
403B GLY 3.5 0.4 + - - -
404B THR 3.3 0.4 - - - -
405B PRO* 1.3 84.0 - - + +
407B ARG* 1.3 60.8 + - - +
409B THR* 3.0 8.2 + - - +
410B TRP* 2.8 30.7 + - - +
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Residues in contact with ARG 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 5.0 5.3 - - - +
306A LEU* 3.5 15.2 - - - +
309A GLU* 3.0 41.0 + - - -
399B GLY* 3.3 31.9 - - - +
402B ILE* 3.7 10.5 - - - +
403B GLY 2.8 21.0 + - - +
404B THR* 3.7 6.7 - - - +
405B PRO 3.4 0.2 - - - -
406B LYS* 1.3 76.5 - - - +
408B GLU* 1.3 59.8 + - - +
410B TRP* 3.2 15.1 + - + +
411B LEU* 2.9 53.3 + - + +
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Residues in contact with GLU 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A VAL* 4.9 0.3 - - - +
306A LEU* 3.7 27.7 - - + +
404B THR* 3.1 20.5 + - + +
405B PRO* 3.6 6.5 - - + +
407B ARG* 1.3 82.9 - - - +
409B THR* 1.3 62.9 - - + +
411B LEU* 3.3 11.4 + - - +
412B GLN* 3.2 35.3 + - - +
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Residues in contact with THR 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B MET* 6.1 4.5 - - - +
311B MET* 3.6 13.4 - - - +
405B PRO 3.3 15.1 + - - +
406B LYS* 3.0 13.7 + - - +
408B GLU* 1.3 78.6 - - + +
410B TRP* 1.3 65.5 + - - +
412B GLN* 3.3 10.2 + - - +
413B LEU* 3.0 25.3 + - - +
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Residues in contact with TRP 410 (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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308B MET* 4.9 6.0 - - + +
311B MET* 3.7 25.1 - - + -
398B VAL* 3.6 44.0 - - + -
399B GLY 4.5 1.1 - - - -
402B ILE* 4.0 4.9 - - + -
406B LYS 2.8 18.7 + - - +
407B ARG* 3.2 28.5 - - + +
409B THR* 1.3 78.4 + - - +
411B LEU* 1.3 84.0 + - + +
413B LEU* 3.6 2.7 + - + +
414B ARG* 3.1 46.6 + - + +
459B LEU 4.3 2.5 - - - -
460B LEU* 3.0 50.4 + - + +
462B GLY* 5.1 2.7 - - - -
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Residues in contact with LEU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 3.9 35.6 - - + +
287A THR* 5.9 1.1 - - + -
302A VAL* 4.3 8.7 - - + -
306A LEU* 3.9 21.8 - - + -
407B ARG* 2.9 50.7 + - - +
408B GLU* 3.7 7.2 - - - +
409B THR 3.2 0.2 - - - -
410B TRP* 1.3 105.3 - - + +
412B GLN* 1.3 65.1 + - - +
414B ARG* 3.4 7.2 + - + +
415B ALA* 3.1 23.4 + - - +
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Residues in contact with GLN 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A THR* 4.7 1.2 + - - +
299A THR* 3.5 45.1 - - - +
302A VAL* 3.9 25.5 - - + +
303A ARG* 4.6 3.3 + - - +
408B GLU* 3.2 35.1 + - - +
409B THR* 3.3 9.3 + - - +
411B LEU* 1.3 76.6 - - - +
413B LEU* 1.3 57.0 + - - +
415B ALA* 3.4 2.9 + - - +
416B GLU* 3.0 38.3 + - + +
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Residues in contact with LEU 413 (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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304B ILE* 3.8 31.1 - - + +
307B MET* 3.8 37.9 - - + -
308B MET* 3.6 41.5 - - + +
311B MET* 3.9 18.8 - - - -
409B THR 3.0 16.7 + - - +
410B TRP* 3.7 5.2 - - + +
411B LEU 3.2 0.2 - - - -
412B GLN* 1.3 76.0 - - - +
414B ARG* 1.3 66.2 + - + +
416B GLU* 3.2 13.4 + - - +
417B LEU* 2.9 25.1 + - + +
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Residues in contact with ARG 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU 5.4 0.9 - - - +
287A THR* 4.0 33.3 + - - +
308B MET* 5.5 6.7 - - - -
410B TRP* 3.1 41.1 + - + +
411B LEU* 3.4 9.2 + - + +
413B LEU* 1.3 79.6 - - + +
415B ALA* 1.3 57.8 + - - +
417B LEU* 3.4 18.0 - - - +
418B GLU* 3.0 42.2 + - - +
425B LEU* 3.4 26.6 - - - +
429B LEU* 5.2 4.4 - - - +
460B LEU 3.2 20.6 + - - -
461B TYR* 3.7 24.5 + - - +
462B GLY* 3.8 9.3 - - - +
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Residues in contact with ALA 415 (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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287A THR 3.7 10.1 + - - -
288A GLY* 3.6 22.5 - - - +
298A THR* 3.6 24.6 - - - +
302A VAL* 3.8 18.2 - - + -
411B LEU 3.1 17.3 + - - +
412B GLN 3.6 5.4 - - - +
413B LEU 3.1 0.2 - - - -
414B ARG* 1.3 75.6 - - - +
416B GLU* 1.3 64.9 + - - +
418B GLU* 3.4 3.3 + - - +
419B ALA* 3.2 16.6 + - - +
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Residues in contact with GLU 416 (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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298A THR* 4.0 19.0 + - - +
299A THR* 5.7 3.4 - - - +
300B THR* 5.5 1.0 - - - +
303B ARG* 2.4 36.8 + - - -
304B ILE* 3.7 14.7 - - + +
307B MET* 5.3 4.2 - - - +
412B GLN* 3.0 27.9 + - + +
413B LEU* 3.6 17.0 - - - +
415B ALA* 1.3 75.0 - - - +
417B LEU* 1.3 53.5 + - - +
419B ALA* 3.2 4.5 + - - +
420B LEU* 2.8 34.1 + - - +
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Residues in contact with LEU 417 (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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281B ILE* 4.3 3.8 - - + +
285B LEU* 3.6 32.1 - - + -
304B ILE* 3.8 17.2 - - + +
308B MET* 5.5 4.3 - - + -
413B LEU* 2.9 17.0 + - + +
414B ARG* 3.4 18.2 - - - +
416B GLU* 1.3 78.7 - - - +
418B GLU* 1.3 59.4 + - - +
420B LEU* 3.0 5.8 + - + +
421B THR* 2.7 59.4 + - + +
425B LEU* 5.7 2.2 - - + -
461B TYR* 3.8 35.4 - - + +
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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
----------------------------------------------------------
287A THR 3.5 19.7 - - - +
288A GLY 4.0 16.2 - - - +
289A THR* 4.6 2.0 - - - +
292A SER* 2.9 8.6 + - - -
414B ARG* 3.0 22.7 + - - +
415B ALA 3.8 5.4 - - - +
416B GLU 3.4 0.4 - - - -
417B LEU* 1.3 81.7 - - - +
419B ALA* 1.3 60.9 + - - +
421B THR* 3.7 5.8 + - - -
422B ASP 3.2 1.6 + - - -
423B LEU* 2.8 44.3 + - + +
425B LEU* 3.3 31.9 + - - +
426B THR* 2.6 31.6 + - - +
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Residues in contact with ALA 419 (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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292A SER* 3.4 19.1 + - - +
298A THR* 3.9 18.8 - - + -
296B LYS* 4.1 2.8 + - - -
415B ALA 3.2 11.3 + - - +
416B GLU* 3.5 7.9 - - - +
417B LEU 3.1 0.4 - - - -
418B GLU* 1.3 77.6 - - - +
420B LEU* 1.3 67.0 + - - +
422B ASP* 3.1 20.4 + - - +
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Residues in contact with LEU 420 (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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285B LEU* 3.7 29.8 - - + -
290B PHE* 3.8 8.5 - - + -
296B LYS* 3.2 59.4 + - + +
297B ASP* 4.7 2.9 - - + +
300B THR* 4.3 19.1 - - + -
301B SER* 3.7 22.7 - - - +
304B ILE* 3.9 17.9 - - + -
416B GLU 2.8 16.3 + - - +
417B LEU* 3.5 9.9 - - + +
419B ALA* 1.3 76.6 - - - +
421B THR* 1.3 57.9 + - + +
422B ASP 3.2 2.1 + - - -
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Residues in contact with THR 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ILE* 3.8 31.6 - - + -
290B PHE* 3.6 21.6 - - + -
417B LEU* 2.7 45.9 + - + +
418B GLU* 3.7 10.4 + - - -
420B LEU* 1.3 74.3 - - + +
422B ASP* 1.3 70.4 + - - +
424B TRP* 3.2 31.7 + - - +
523B HIS* 3.7 8.0 - - - -
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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