Contacts of the helix formed by residues 406 - 422 (chain B) in PDB entry 3SRH
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 ASP 406 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A CYS* 5.2 1.1 - - - +
404B THR* 2.9 19.0 + - - +
405B SER* 1.3 77.7 + - - +
407B PRO* 1.3 73.9 - - - +
408B THR* 2.6 33.5 + - - +
409B GLU* 3.3 19.2 + - + +
410B ALA* 3.4 10.1 + - - +
435B ARG* 3.1 23.2 + - - -
439B GLN* 3.6 3.1 + - - -
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Residues in contact with PRO 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A CYS* 6.0 0.2 - - + -
507A VAL* 4.6 14.1 - - + -
526A VAL* 3.8 37.1 - - + +
528A PRO* 5.4 10.1 - - + -
405B SER 3.3 10.3 - - - +
406B ASP* 1.3 92.7 - - - +
408B THR* 1.3 54.1 + - + +
410B ALA* 3.4 4.6 + - + +
411B THR* 2.6 37.0 + - - -
521B THR 4.4 0.4 - - - -
522B ASN* 5.2 4.0 - - + -
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Residues in contact with THR 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B ASP* 2.6 30.9 + - - +
407B PRO* 1.3 79.9 - - + +
409B GLU* 1.3 56.5 + - - +
411B THR* 3.3 3.3 + - - -
412B ALA* 3.0 27.5 + - - +
435B ARG* 3.8 8.9 + - - +
436B SER* 5.7 0.2 - - - -
439B GLN* 3.2 22.6 + - - +
519B GLY 3.3 26.2 - - - +
520B PHE* 3.9 7.0 - - - -
521B THR* 3.3 30.6 - - - +
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Residues in contact with GLU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LYS* 3.7 22.2 - - - +
404B THR* 3.6 20.9 - - + +
406B ASP* 3.3 12.7 + - - +
408B THR* 1.3 80.8 + - - +
410B ALA* 1.3 62.1 + - - +
412B ALA* 3.3 10.9 + - - +
413B VAL* 3.2 18.5 + - - +
435B ARG* 5.0 0.2 + - - -
439B GLN* 2.8 35.3 + - - +
442B ARG* 3.9 19.8 + - - -
443B TYR* 3.0 31.8 + - - -
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Residues in contact with ALA 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ALA* 3.4 23.5 - - + +
421A LYS* 4.0 6.8 - - + +
422A CYS* 3.9 35.7 - - + -
526A VAL* 4.3 9.9 - - + -
404B THR* 5.1 0.2 - - + -
406B ASP 3.4 5.6 + - - +
407B PRO 3.4 8.7 + - - +
408B THR 3.3 0.4 - - - -
409B GLU* 1.3 76.0 - - - +
411B THR* 1.3 64.6 + - - +
413B VAL* 3.4 10.9 - - - +
414B GLY 3.3 16.3 + - - -
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Residues in contact with THR 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A MET* 4.1 16.0 - - + +
526A VAL* 3.4 11.6 - - - +
407B PRO 2.6 21.2 + - - -
408B THR 3.4 7.4 - - - -
410B ALA* 1.3 77.2 - - - +
412B ALA* 1.3 63.9 + - - +
414B GLY* 3.4 1.7 + - - -
415B ALA* 3.0 23.8 + - - +
511B LEU* 3.7 24.5 - - + -
521B THR* 3.3 18.3 + - + +
522B ASN* 3.4 29.8 - - - +
523B THR 4.3 0.4 - - - +
524B MET* 4.4 1.3 - - + -
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Residues in contact with ALA 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B THR 3.0 13.4 + - - +
409B GLU* 3.3 10.3 + - - +
411B THR* 1.3 77.8 - - - +
413B VAL* 1.3 62.9 + - - +
415B ALA* 3.4 4.6 + - - +
416B VAL* 3.1 27.5 + - - +
436B SER 5.2 0.2 - - - +
439B GLN* 3.5 40.4 - - + +
440B VAL* 4.1 12.7 - - + +
443B TYR* 4.5 3.8 - - + -
511B LEU* 4.9 3.1 - - + -
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Residues in contact with VAL 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A GLU* 4.0 20.0 - - + +
418A ALA* 4.9 0.7 - - - -
421A LYS* 3.6 30.7 - - + -
394B PHE* 4.4 10.5 - - + -
398B ARG* 4.6 4.9 - - + -
409B GLU 3.2 17.0 - - - +
410B ALA 3.4 13.5 - - - +
412B ALA* 1.3 71.7 - - - +
414B GLY* 1.3 55.0 - - - +
416B VAL* 3.0 8.1 + - - +
417B GLU* 2.7 35.2 + - - +
443B TYR* 3.3 42.8 - - + +
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Residues in contact with GLY 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A GLY* 3.5 30.1 - - - -
417A GLU* 4.2 6.9 - - - +
418A ALA* 4.5 1.3 - - - +
524A MET* 5.0 2.0 - - - -
410B ALA 3.3 12.6 + - - -
411B THR 3.8 2.9 - - - -
413B VAL* 1.3 78.6 - - - +
415B ALA* 1.3 52.1 + - - +
417B GLU* 3.3 0.3 + - - +
418B ALA* 2.8 36.0 + - - +
524B MET* 4.0 8.1 - - - -
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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
----------------------------------------------------------
411B THR 3.0 13.8 + - - +
412B ALA 3.4 9.9 - - - +
414B GLY* 1.3 75.3 - - - +
416B VAL* 1.3 52.0 + - + +
418B ALA* 3.4 2.3 + - - +
419B SER* 2.8 34.6 + - - -
427B ILE* 4.6 7.2 - - + -
440B VAL* 5.1 1.1 - - + -
509B ILE* 3.8 16.6 - - + +
511B LEU* 3.8 31.4 - - + -
524B MET* 3.7 13.6 - - + -
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Residues in contact with VAL 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B PHE* 3.7 18.8 - - + -
412B ALA 3.1 17.1 + - - +
413B VAL* 3.0 8.1 + - - +
415B ALA* 1.3 72.3 - - - +
417B GLU* 1.3 64.8 + - - +
419B SER* 3.0 20.9 - - - -
420B PHE* 3.1 32.3 + - + -
427B ILE* 4.4 1.1 - - - -
440B VAL* 3.8 37.0 - - + +
443B TYR* 3.9 18.2 - - + +
445B PRO* 4.0 13.5 - - + -
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Residues in contact with GLU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A PHE* 4.9 1.1 - - + -
398A ARG* 2.8 50.6 + - - +
413A VAL* 4.0 29.0 - - + +
417A GLU* 3.5 32.7 - - + +
394B PHE* 3.3 16.6 - - + -
413B VAL 2.7 19.4 + - - +
414B GLY 3.6 4.0 - - - +
416B VAL* 1.3 71.8 - - - +
418B ALA* 1.3 63.5 + - - +
420B PHE* 3.0 10.9 + - - +
421B LYS* 3.0 24.1 + - - +
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Residues in contact with ALA 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ALA* 3.4 29.6 - - + +
413A VAL* 4.9 0.2 - - - -
414A GLY* 4.6 1.3 - - - -
414B GLY 2.8 20.2 + - - +
415B ALA 3.6 4.5 - - - +
417B GLU* 1.3 72.7 - - - +
419B SER* 1.3 62.6 + - - +
421B LYS* 3.0 14.9 + - - +
422B CYS* 3.1 19.1 + - - -
509B ILE* 3.8 18.6 - - + -
524B MET* 4.0 14.6 - - + -
526B VAL* 5.0 0.2 - - + -
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Residues in contact with SER 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B ALA 2.8 18.9 + - - -
416B VAL* 3.0 15.1 + - - -
418B ALA* 1.3 73.0 - - - +
420B PHE* 1.3 61.2 + - - -
423B CYS* 3.2 3.3 + - - -
424B SER* 2.9 37.7 + - - -
427B ILE* 3.7 24.3 - - - +
445B PRO* 4.0 7.1 - - - +
446B ARG* 5.0 2.8 + - - +
447B ALA* 3.5 23.2 + - - +
509B ILE* 4.0 2.4 - - - +
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Residues in contact with PHE 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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398A ARG* 4.9 5.4 - - - +
403A ILE* 4.1 14.9 - - - +
390B HIS* 3.9 28.7 - + + -
394B PHE* 3.8 34.8 - + + -
416B VAL* 3.1 42.4 + - + -
417B GLU* 3.0 13.0 + - - +
419B SER* 1.3 77.1 - - - +
421B LYS* 1.3 64.2 + - - +
423B CYS* 3.4 10.6 + - - +
444B ARG 3.9 20.4 - - - -
445B PRO* 3.9 6.1 - - + -
446B ARG* 4.0 33.0 - - + -
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Residues in contact with LYS 421 (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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398A ARG 4.7 4.9 + - - +
401A ALA* 3.3 33.1 + - - +
402A PRO 2.8 27.2 + - - +
403A ILE* 3.4 14.0 - - + +
404A THR* 3.4 26.0 + - + -
409A GLU* 3.9 16.5 - - - +
410A ALA* 3.9 13.5 - - + +
413A VAL* 3.6 30.1 - - + -
442A ARG* 5.6 0.4 - - - +
443A TYR* 3.3 18.5 + - - +
417B GLU* 3.0 17.0 + - - +
418B ALA* 3.0 8.7 + - - +
420B PHE* 1.3 77.2 - - - +
422B CYS* 1.3 57.0 + - - +
423B CYS 3.3 0.2 - - - -
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Residues in contact with CYS 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ILE* 4.4 2.8 - - - +
404A THR 3.3 19.7 - - - +
405A SER* 5.1 3.7 - - - -
406A ASP 5.2 2.0 - - - +
410A ALA* 3.9 18.2 - - + -
418B ALA 3.1 19.5 + - - -
421B LYS* 1.3 74.9 - - - +
423B CYS* 1.3 70.1 + - - +
424B SER* 3.2 21.2 + - - -
507B VAL* 3.7 36.7 - - + +
509B ILE* 4.1 13.2 - - - -
526B VAL* 4.7 0.2 - - - -
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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