Contacts of the helix formed by residues 412 - 423 (chain A) in PDB entry 3D7T
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 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A GLY* 6.2 1.3 - - - -
380A TYR* 4.1 17.5 - - + -
410A GLY 3.6 8.3 - - - +
411A CYS* 1.3 91.3 - - - +
413A PRO* 1.3 76.3 - - + +
414A ALA 3.1 0.4 - - - +
415A VAL* 2.8 30.7 + - + +
416A TYR 3.3 6.8 + - - -
448A LEU 3.6 23.1 - - - +
449A HIS* 3.9 23.3 - - + +
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Residues in contact with PRO 413 (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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411A CYS 3.4 6.9 - - - +
412A PRO* 1.3 83.5 - - + +
414A ALA* 1.3 64.7 + - - +
416A TYR* 3.1 20.1 + - + +
417A GLU* 3.3 22.5 + - - +
448A LEU 5.5 0.9 - - - +
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Residues in contact with ALA 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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412A PRO 3.0 0.4 + - - -
413A PRO* 1.3 81.9 - - - +
415A VAL* 1.3 60.7 + - - +
417A GLU* 3.7 12.9 - - - +
418A VAL* 3.6 13.5 + - - +
443A ILE* 3.4 35.4 - - + +
448A LEU* 3.9 34.3 - - + +
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Residues in contact with VAL 415 (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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292A LEU* 5.3 4.3 - - + -
376A LEU* 4.3 12.3 - - + -
380A TYR* 3.5 46.0 - - + +
411A CYS* 4.0 8.7 - - - -
412A PRO* 2.8 30.8 + - + +
414A ALA* 1.3 75.7 - - - +
416A TYR* 1.3 63.8 + - - +
418A VAL* 3.0 23.5 + - + +
419A MET* 3.2 11.4 + - + +
440A LEU* 6.1 3.6 - - + -
443A ILE* 4.2 22.0 - - + -
448A LEU 5.1 0.2 - - - +
449A HIS* 5.2 3.1 - - + -
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Residues in contact with TYR 416 (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 LYS* 4.9 4.2 + - - +
405A MET 2.9 27.9 + - - -
406A ASP* 3.8 3.8 + - - -
407A ALA* 3.4 43.9 + - + -
408A PRO* 4.4 0.9 - - + -
411A CYS* 4.1 4.5 - - - +
412A PRO 3.3 6.1 + - - +
413A PRO* 3.1 13.7 + - + +
415A VAL* 1.3 77.9 - - - +
417A GLU* 1.3 56.1 + - + +
419A MET* 3.2 23.2 - - + +
420A LYS* 2.9 65.9 + - + +
423A TRP* 4.5 8.3 - + - -
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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
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413A PRO* 3.3 19.7 + - - +
414A ALA* 3.7 12.1 - - - +
415A VAL 3.2 0.2 - - - -
416A TYR* 1.3 73.2 - - + +
418A VAL* 1.3 56.2 + - - +
419A MET 3.1 1.6 - - - -
420A LYS* 3.8 21.4 - - - +
421A ASN* 2.7 36.8 + - - +
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Residues in contact with VAL 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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372A PHE* 5.3 2.5 - - + -
376A LEU* 3.5 22.4 - - + -
414A ALA 3.6 14.3 + - - +
415A VAL* 3.0 11.3 + - - +
417A GLU* 1.3 76.0 - - - +
419A MET* 1.3 57.1 + - - +
421A ASN* 3.0 15.5 - - - +
422A CYS* 2.7 29.7 - - - -
436A LEU* 3.8 22.7 - - + -
439A GLN* 4.0 19.5 - - + +
440A LEU* 4.2 19.1 - - + -
443A ILE* 4.0 17.5 - - + -
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Residues in contact with MET 419 (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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373A GLY* 3.7 8.5 - - - +
376A LEU* 3.5 25.8 - - + -
377A TRP* 3.4 37.5 - - - +
380A TYR* 5.0 0.7 - - + -
408A PRO* 3.7 27.8 - - + -
411A CYS* 3.8 13.5 - - - -
415A VAL* 3.2 10.5 + - + +
416A TYR* 3.2 40.2 - - + +
417A GLU 3.1 0.2 - - - -
418A VAL* 1.3 74.1 - - - +
420A LYS* 1.3 66.9 + - - +
421A ASN 3.0 1.6 - - - -
422A CYS* 2.8 20.2 + - - +
423A TRP* 3.2 33.1 + - + -
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Residues in contact with LYS 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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404A LYS* 4.0 23.6 + - + -
416A TYR* 2.9 66.9 + - + +
417A GLU* 3.8 20.9 - - - +
419A MET* 1.3 72.1 - - - +
421A ASN* 1.3 62.4 + - - +
423A TRP* 3.1 28.9 + - + +
424A HIS* 3.8 9.6 + - - -
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Residues in contact with ASN 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 2.7 19.2 + - - +
418A VAL* 3.0 11.9 - - - +
420A LYS* 1.3 77.8 - - - +
422A CYS* 1.3 57.8 + - - +
423A TRP 3.1 1.2 + - - -
424A HIS* 3.3 46.3 + - - -
429A MET 4.6 0.5 - - - +
430A ARG* 3.8 1.4 - - - -
431A PRO* 3.5 30.5 - - + +
439A GLN* 3.3 35.2 + - - +
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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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369A VAL* 3.0 37.0 - - + +
370A TRP* 3.5 15.1 - - - -
372A PHE* 4.8 4.3 - - - -
373A GLY* 3.9 16.8 - - - -
376A LEU* 5.5 0.2 - - - -
418A VAL* 2.7 36.1 - - - -
419A MET* 2.8 13.4 + - - +
421A ASN* 1.3 71.6 - - - +
423A TRP* 1.3 56.9 + - - +
424A HIS 3.4 1.8 - - - -
430A ARG* 3.1 20.9 - - - -
431A PRO* 4.5 0.7 - - - -
436A LEU* 3.8 26.2 - - - -
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Residues in contact with TRP 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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370A TRP* 3.2 47.7 + + + -
373A GLY* 3.1 29.0 - - - -
374A ILE* 3.2 36.8 - - + +
377A TRP* 4.1 4.7 - + + -
387A TYR* 5.6 1.1 - - - -
404A LYS* 2.7 48.7 + - + +
405A MET* 3.8 39.9 - - + -
416A TYR* 4.5 6.1 - + - -
419A MET* 3.4 39.5 - - + -
420A LYS* 3.1 11.4 + - - +
421A ASN 3.0 2.0 - - - -
422A CYS* 1.3 86.3 - - - +
424A HIS* 1.3 59.4 + - - +
425A LEU* 3.5 3.1 + - - +
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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
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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