Contacts of the helix formed by residues 408 - 423 (chain A) in PDB entry 4QGC
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 408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407A ASP* 1.3 91.4 - - - +
409A THR* 1.3 53.1 + - - +
411A ALA* 3.5 1.8 + - + +
412A THR* 2.7 38.5 + - - -
521A PHE* 4.0 17.9 - - + -
523A ASN* 4.2 1.6 - - + -
508B VAL* 5.1 10.7 - - + -
527B VAL* 3.3 42.9 - - + +
529B PRO* 4.3 20.4 - - + -
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Residues in contact with THR 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASP* 3.1 12.8 + - - -
408A PRO* 1.3 77.6 - - - +
410A GLU* 1.3 58.3 + - - +
412A THR* 3.6 2.1 + - - -
413A ALA* 3.2 25.3 + - - +
436A ARG* 3.9 18.0 + - - +
437A SER* 4.8 6.1 - - - -
440A GLN* 3.2 21.9 - - - +
521A PHE* 3.2 28.9 - - + +
522A THR* 3.3 35.4 - - - +
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Residues in contact with GLU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A PRO 6.4 2.7 - - - -
407A ASP* 3.2 26.7 + - + +
409A THR* 1.3 77.8 - - - +
411A ALA* 1.3 64.3 + - - +
413A ALA* 3.2 4.9 + - - +
414A VAL* 3.1 26.0 + - + +
440A GLN* 3.2 33.4 + - - +
443A ARG* 3.7 11.5 + - - +
444A TYR* 2.2 41.7 + - - +
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Residues in contact with ALA 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASP 3.1 15.1 + - - +
408A PRO 3.9 4.9 - - - +
410A GLU* 1.3 76.2 - - - +
412A THR* 1.3 58.1 + - - +
414A VAL* 3.6 7.5 + - - +
415A GLY* 3.0 24.1 + - - -
419B ALA* 5.7 4.2 - - + +
422B ARG* 5.3 9.3 + - - +
423B CYS* 3.6 29.8 - - - -
525B MET* 5.4 2.8 - - - +
527B VAL* 4.3 13.5 - - + +
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Residues in contact with THR 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A PRO 2.7 22.1 + - - -
409A THR 3.8 5.4 - - - -
410A GLU 3.2 0.2 - - - -
411A ALA* 1.3 75.6 - - - +
413A ALA* 1.3 58.6 + - - +
415A GLY* 3.4 1.7 + - - -
416A ALA* 3.0 28.6 + - - +
512A LEU* 4.0 26.0 - - + -
522A THR* 3.8 10.8 - - + +
523A ASN* 3.3 34.4 + - - +
524A THR 4.0 2.0 - - - +
525A MET* 4.2 11.3 - - + +
525B MET* 5.5 5.2 - - + +
527B VAL* 3.8 10.6 - - - +
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Residues in contact with ALA 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A THR 3.2 14.6 + - - +
410A GLU* 3.2 9.4 + - - +
412A THR* 1.3 74.8 - - - +
414A VAL* 1.3 64.5 + - - +
416A ALA* 3.3 3.8 + - - +
417A VAL* 3.2 27.8 + - - +
437A SER 5.1 0.2 - - - +
440A GLN* 4.1 26.2 - - + +
441A VAL* 4.0 25.3 - - + +
444A TYR* 4.3 5.4 - - + -
512A LEU* 4.5 3.4 - - + -
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Residues in contact with VAL 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A PHE* 4.1 4.3 - - + -
399A ARG* 4.1 17.3 - - + -
410A GLU* 3.1 18.8 + - + +
411A ALA* 3.9 4.9 - - - +
413A ALA* 1.3 74.5 - - - +
415A GLY* 1.3 58.4 + - - +
417A VAL* 3.3 6.0 + - - +
418A GLU* 2.9 28.9 + - + +
444A TYR* 3.4 42.6 - - + +
422B ARG* 3.6 43.7 - - - +
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Residues in contact with GLY 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ALA 3.0 17.6 + - - -
412A THR* 3.8 1.8 - - - -
413A ALA 3.3 0.4 - - - -
414A VAL* 1.3 77.0 - - - +
416A ALA* 1.3 56.3 + - - +
418A GLU* 3.3 11.0 - - - +
419A ALA* 2.9 29.5 + - - +
422A ARG* 5.1 0.7 + - - -
525A MET* 3.7 15.6 - - - +
415B GLY 6.2 0.4 - - - -
419B ALA* 6.2 2.2 - - - -
422B ARG* 5.0 5.6 - - - -
525B MET* 5.4 5.8 - - - -
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Residues in contact with ALA 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A THR 3.0 17.9 + - - +
413A ALA 3.6 5.6 - - - +
414A VAL 3.2 0.4 - - - -
415A GLY* 1.3 73.9 - - - +
417A VAL* 1.3 59.1 + - - +
419A ALA* 3.4 2.9 + - - +
420A SER* 3.0 27.4 + - - -
428A ILE* 3.8 12.2 - - + +
441A VAL* 5.1 0.7 - - + -
510A ILE* 4.0 12.9 - - + +
512A LEU* 3.7 33.9 - - + -
525A MET* 3.5 10.2 - - - -
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Residues in contact with VAL 417 (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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395A PHE* 3.6 29.4 - - + -
413A ALA 3.2 14.6 + - - +
414A VAL 3.7 6.1 - - - +
416A ALA* 1.3 72.7 - - - +
418A GLU* 1.3 65.8 + - - +
420A SER* 2.5 22.4 + - - -
421A PHE* 3.2 27.9 + - + -
428A ILE* 4.1 1.6 - - + -
441A VAL* 3.7 34.8 - - + +
444A TYR* 4.0 11.7 - - + +
446A PRO* 3.8 17.7 - - + -
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Residues in contact with GLU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A PHE* 3.6 18.7 - - + -
399A ARG* 2.2 36.1 + - - -
414A VAL* 2.9 20.8 + - + +
415A GLY* 3.3 13.5 - - - +
417A VAL* 1.3 78.3 - - - +
419A ALA* 1.3 57.6 + - - +
421A PHE* 3.3 4.9 + - - +
422A ARG* 2.9 43.0 + - - +
418B GLU* 2.8 19.7 - - - +
422B ARG* 2.6 21.4 + - - +
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Residues in contact with ALA 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A GLY 2.9 16.9 + - - +
416A ALA 3.8 4.9 - - - +
418A GLU* 1.3 75.9 - - - +
420A SER* 1.3 55.2 + - - +
422A ARG* 3.8 19.5 - - - +
423A CYS* 2.7 44.2 + - - +
425A SER* 4.3 1.6 - - - -
510A ILE* 3.8 18.2 - - + -
525A MET* 4.4 13.0 - - + -
527A VAL* 5.1 4.3 - - + -
411B ALA* 5.8 2.2 - - + +
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Residues in contact with SER 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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416A ALA 3.0 15.2 + - - -
417A VAL* 2.5 24.8 + - - -
419A ALA* 1.3 75.8 - - - +
421A PHE* 1.3 60.0 + - - +
424A CYS* 3.2 6.8 + - - -
425A SER* 3.0 41.5 + - - +
428A ILE* 3.8 21.8 - - - -
446A PRO* 3.9 13.2 - - - +
447A ARG 5.2 0.3 + - - -
448A ALA* 4.3 10.6 + - - +
510A ILE* 4.3 0.7 - - - -
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Residues in contact with PHE 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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391A HIS* 4.1 23.1 - - + -
392A LEU* 3.6 33.4 - - + -
395A PHE* 3.9 24.5 - + + -
417A VAL* 3.2 42.0 + - + -
418A GLU* 3.7 5.4 - - - +
420A SER* 1.3 82.7 + - - +
422A ARG* 1.3 65.7 + - - +
424A CYS* 3.5 16.5 + - - +
445A ARG 4.3 0.9 - - - -
446A PRO* 4.0 7.2 - - + -
447A ARG* 3.6 53.4 + - + +
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Residues in contact with ARG 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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415A GLY 5.1 0.4 + - - -
418A GLU* 2.9 32.4 + - - +
419A ALA* 3.2 27.4 + - - +
421A PHE* 1.3 79.6 - - - +
423A CYS* 1.3 66.1 + - - +
424A CYS* 3.7 4.2 + - - -
399B ARG* 5.3 5.0 - - - +
411B ALA* 4.1 11.5 + - - +
414B VAL* 3.6 30.5 - - - +
415B GLY* 3.8 20.4 - - - +
418B GLU* 2.9 42.1 + - - +
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Residues in contact with CYS 423 (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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419A ALA* 2.7 31.3 + - - +
422A ARG* 1.3 80.4 - - - +
424A CYS* 1.3 70.3 + - - +
425A SER* 3.4 13.5 + - - +
508A VAL* 4.9 18.7 - - + +
510A ILE* 4.8 0.7 - - - -
527A VAL* 4.7 11.7 - - - -
406B SER* 5.9 9.4 - - - +
411B ALA* 3.5 31.4 - - - -
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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
------------------------------------------------------------
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