Contacts of the helix formed by residues 406 - 422 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404A THR* 3.2 23.1 + - + +
405A SER* 1.3 77.3 + - - +
407A PRO* 1.3 72.4 - - - +
408A THR* 2.7 23.2 + - - +
409A GLU* 3.2 16.1 + - + +
410A ALA* 3.2 13.4 + - - +
435A ARG* 2.8 31.5 + - - -
439A GLN* 3.6 6.2 + - - -
422B CYS* 5.7 0.4 - - - -
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Residues in contact with PRO 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A SER 3.1 11.8 - - - +
406A ASP* 1.3 87.1 - - - +
408A THR* 1.3 59.7 + - + +
410A ALA* 3.3 4.0 + - + +
411A THR* 2.7 39.2 + - - -
519A GLY 6.0 0.9 - - - +
521A THR 4.4 0.7 - - - -
522A ASN* 4.9 5.8 - - + -
422B CYS* 5.9 0.4 - - + -
507B VAL* 4.9 5.2 - - + -
526B VAL* 3.6 38.1 - - + +
527B VAL* 6.0 0.2 - - - -
528B PRO* 6.3 2.5 - - + -
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Residues in contact with THR 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ASP* 2.7 32.7 + - - +
407A PRO* 1.3 80.7 - - + +
409A GLU* 1.3 55.8 + - - +
411A THR* 3.4 3.3 + - - -
412A ALA* 3.0 26.9 + - - +
435A ARG* 3.1 14.5 + - - +
436A SER* 5.5 0.9 - - - +
439A GLN* 3.2 17.7 + - - +
519A GLY* 3.8 20.6 - - - +
520A PHE 4.5 0.7 - - - -
521A THR* 3.3 45.1 - - - +
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Residues in contact with GLU 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A THR* 3.8 21.3 - - + -
406A ASP* 3.2 21.2 + - + +
408A THR* 1.3 79.8 + - - +
410A ALA* 1.3 62.9 + - - +
412A ALA* 3.3 10.0 + - - +
413A VAL* 3.2 19.7 + - - +
435A ARG* 5.2 0.2 + - - -
439A GLN* 3.0 34.4 + - - +
442A ARG* 3.7 20.2 + - - +
443A TYR* 2.9 31.0 + - - -
421B LYS* 3.9 13.5 - - - -
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Residues in contact with ALA 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A THR 5.7 0.2 - - - +
406A ASP 3.2 8.8 + - - +
407A PRO 3.3 7.4 + - - +
409A GLU* 1.3 75.6 - - - +
411A THR* 1.3 62.9 + - - +
413A VAL* 3.4 10.9 - - - +
414A GLY* 3.3 16.1 + - - -
418B ALA* 3.4 25.6 - - + +
421B LYS* 3.9 8.6 - - + +
422B CYS* 3.9 31.4 - - + -
526B VAL* 4.4 10.3 - - + -
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Residues in contact with THR 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A PRO 2.7 22.3 + - - -
408A THR 3.6 5.2 - - - -
410A ALA* 1.3 75.7 - - - +
412A ALA* 1.3 58.3 + - - +
414A GLY* 3.4 1.2 + - - -
415A ALA* 3.1 28.1 + - - +
511A LEU* 3.7 21.7 - - + +
521A THR* 3.9 10.5 - - + +
522A ASN* 3.3 13.9 - - - -
523A THR 3.7 27.1 - - - +
524A MET* 4.9 0.2 - - - +
524B MET* 4.1 17.7 - - + +
526B VAL* 3.3 12.9 - - - +
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Residues in contact with ALA 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A THR 3.0 14.5 + - - +
409A GLU* 3.3 11.6 + - - +
411A THR* 1.3 73.7 - - - +
413A VAL* 1.3 65.7 + - - +
415A ALA* 3.3 7.0 + - - +
416A VAL* 3.2 26.7 + - - +
436A SER 5.4 0.4 - - - +
439A GLN* 3.7 38.4 - - + +
440A VAL* 4.3 12.4 - - + +
443A TYR* 4.5 3.4 - - + -
511A LEU* 4.8 2.5 - - - -
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Residues in contact with VAL 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A PHE* 4.4 8.8 - - + -
398A ARG* 4.8 4.3 - - + -
409A GLU 3.2 16.6 - - - +
410A ALA 3.4 13.7 - - - +
412A ALA* 1.3 72.0 - - - +
414A GLY* 1.3 53.9 + - - +
416A VAL* 3.1 5.9 + - - +
417A GLU* 2.7 36.6 + - - +
443A TYR* 3.4 41.7 - - + +
417B GLU* 4.0 22.8 - - + +
418B ALA* 4.9 0.2 - - - -
421B LYS* 3.6 31.2 - - + -
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Residues in contact with GLY 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A ALA 3.3 12.0 + - - -
411A THR 3.7 4.0 - - - -
412A ALA 3.3 0.8 - - - -
413A VAL* 1.3 77.2 - - - +
415A ALA* 1.3 56.5 + - - +
417A GLU* 4.5 1.1 - - - -
418A ALA* 3.0 31.2 + - - +
524A MET* 3.8 8.5 - - - -
414B GLY* 3.5 31.1 - - - -
417B GLU* 4.6 0.8 - - - +
418B ALA* 4.6 3.1 - - - +
524B MET* 4.8 3.1 - - - -
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Residues in contact with ALA 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A THR 3.1 13.4 + - - +
412A ALA 3.5 9.6 - - - +
413A VAL 3.2 0.2 - - - -
414A GLY* 1.3 77.0 - - - +
416A VAL* 1.3 56.9 + - + +
418A ALA* 3.7 2.1 - - - +
419A SER* 2.9 27.7 + - - -
427A ILE* 4.4 8.4 - - + +
440A VAL* 5.0 0.9 - - + -
509A ILE* 3.8 16.8 - - + +
511A LEU* 3.7 33.2 - - + -
524A MET* 3.8 10.9 - - - -
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Residues in contact with VAL 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A PHE* 3.7 16.8 - - + -
412A ALA 3.3 15.5 - - - +
413A VAL* 3.1 6.7 + - - +
415A ALA* 1.3 71.1 - - - +
417A GLU* 1.3 66.2 + - - +
419A SER* 3.1 20.1 - - - -
420A PHE* 3.1 34.7 + - + -
427A ILE* 4.6 0.9 - - - -
440A VAL* 3.7 37.5 - - + +
443A TYR* 3.9 14.1 - - + +
445A PRO* 3.8 19.1 - - + -
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Residues in contact with GLU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A PHE* 3.2 19.3 - - + -
413A VAL 2.7 20.6 + - - +
414A GLY 3.8 3.8 - - - +
416A VAL* 1.3 72.4 - - - +
418A ALA* 1.3 63.1 + - - +
420A PHE* 3.2 6.4 + - - +
421A LYS* 3.1 21.9 + - - +
394B PHE* 4.8 1.1 - - + -
398B ARG* 2.9 49.8 + - - +
413B VAL* 4.0 28.6 - - + +
414B GLY* 4.3 0.4 - - - -
417B GLU* 3.5 34.7 - - + +
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Residues in contact with ALA 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A GLY 3.0 18.6 + - - +
415A ALA 3.7 4.0 - - - +
417A GLU* 1.3 76.6 - - - +
419A SER* 1.3 63.3 + - - +
421A LYS* 3.1 16.7 + - - +
422A CYS* 3.1 17.5 + - - -
509A ILE* 3.8 18.8 - - + -
524A MET* 3.9 12.6 - - + -
526A VAL* 4.9 0.2 - - + -
410B ALA* 3.4 30.1 - - + +
414B GLY* 4.5 0.4 - - - -
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Residues in contact with SER 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ALA 2.9 15.7 + - - -
416A VAL* 3.1 15.9 - - - -
418A ALA* 1.3 76.8 - - - +
420A PHE* 1.3 55.0 + - - +
423A CYS* 3.2 7.6 + - - -
424A SER* 3.1 30.0 + - - -
427A ILE* 3.5 19.0 - - - +
445A PRO* 4.0 7.1 - - - +
446A ARG 5.1 0.3 + - - -
447A ALA* 3.3 29.3 + - - +
509A ILE* 4.1 10.5 - - - +
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Residues in contact with PHE 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A HIS* 4.0 20.6 - - + -
394A PHE* 3.8 36.6 - + + -
416A VAL* 3.1 38.2 + - + -
417A GLU* 3.2 6.7 + - - +
419A SER* 1.3 77.0 - - - +
421A LYS* 1.3 66.2 + - - +
422A CYS 3.4 0.3 + - - -
423A CYS* 3.4 9.2 + - - +
444A ARG 3.6 8.5 - - - -
445A PRO* 3.6 19.5 - - + -
446A ARG* 3.6 38.6 - - + -
398B ARG* 4.8 10.5 - - - +
403B ILE* 4.1 14.2 - - - +
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Residues in contact with LYS 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A GLU* 3.1 15.3 + - - +
418A ALA* 3.1 10.6 + - - +
420A PHE* 1.3 77.6 - - - +
422A CYS* 1.3 56.8 + - - +
398B ARG* 5.0 5.9 + - + +
401B ALA* 3.4 23.0 + - - +
402B PRO* 2.8 26.7 + - - +
403B ILE* 3.3 11.2 - - - +
404B THR* 3.0 37.1 + - + -
409B GLU* 3.7 19.3 + - - +
410B ALA* 4.0 7.9 - - - -
413B VAL* 3.6 27.4 - - + -
443B TYR* 3.2 27.4 + - + +
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Residues in contact with CYS 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A ALA 3.1 18.8 + - - -
421A LYS* 1.3 75.9 - - - +
423A CYS* 1.3 70.4 + - - +
424A SER* 3.1 21.9 + - - -
507A VAL* 3.6 34.8 - - + +
509A ILE* 4.1 8.3 - - - -
403B ILE* 4.1 1.3 - - - +
404B THR* 3.1 22.5 - - + +
405B SER* 5.1 4.1 - - - -
406B ASP 5.2 2.5 - - - +
410B ALA* 3.9 20.0 - - + -
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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