Contacts of the helix formed by residues 403 - 416 (chain A) in PDB entry 6DGD
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 SER 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A LEU* 4.1 16.0 - - - +
392A ASP 5.0 4.9 + - - -
393A LEU* 4.5 13.2 - - - -
396A GLN* 5.0 5.1 - - - +
397A PRO 5.0 0.2 - - - -
398A LEU* 5.8 0.4 - - - -
402A LEU* 1.3 72.9 - - - +
404A PRO* 1.3 74.6 - - - +
405A ALA* 3.7 9.7 + - - +
406A LEU* 2.8 17.1 + - - +
407A ILE* 2.9 15.3 + - - +
596A GLN* 3.1 29.2 - - - +
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Residues in contact with PRO 404 (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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396A GLN* 4.3 16.2 - - + -
397A PRO* 3.5 31.9 - - + +
399A GLN* 6.4 0.7 - - + -
402A LEU 4.1 0.7 - - - +
403A SER* 1.3 87.3 - - - +
405A ALA* 1.3 56.5 + - - +
406A LEU 2.8 6.8 + - - -
407A ILE* 3.1 12.9 + - + +
408A SER* 2.8 28.4 + - - -
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Residues in contact with ALA 405 (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 LEU* 3.9 26.8 - - + +
403A SER* 3.3 6.2 + - - +
404A PRO* 1.3 76.5 - - - +
406A LEU* 1.3 55.6 + - - +
408A SER* 3.6 9.6 + - - -
409A ARG* 3.6 15.9 - - - +
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Residues in contact with LEU 406 (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 LEU* 3.6 11.8 - - + +
402A LEU* 4.0 15.7 - - + -
403A SER 2.8 8.9 + - - +
404A PRO 2.8 0.8 + - - -
405A ALA* 1.3 78.1 - - - +
407A ILE* 1.3 53.8 + - - +
408A SER 3.1 1.6 - - - -
409A ARG* 3.0 7.4 + - + -
410A MET* 2.5 66.1 + - + +
422A LEU* 5.1 0.4 - - + -
552A LEU* 6.0 0.7 - - + -
554A SER* 3.0 35.2 - - - +
556A LEU* 5.3 0.7 - - + -
594A ILE* 3.3 28.3 - - + -
596A GLN* 3.9 26.7 - - + +
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Residues in contact with ILE 407 (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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399A GLN* 3.9 20.9 - - + +
402A LEU* 3.4 39.7 - - + +
403A SER 2.9 27.6 + - - +
404A PRO* 3.1 9.8 + - + +
406A LEU* 1.3 70.7 - - - +
408A SER* 1.3 57.9 + - - +
410A MET* 2.9 10.4 + - - +
411A ARG* 2.9 50.3 + - - +
500A LEU* 4.3 11.7 - - + -
501A PHE* 3.6 26.2 - - + -
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Residues in contact with SER 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A PRO 2.8 18.5 + - - -
405A ALA* 3.6 10.4 + - - -
407A ILE* 1.3 77.1 - - - +
409A ARG* 1.3 60.9 + - - -
410A MET 3.2 0.9 + - - -
411A ARG* 3.3 15.4 - - - +
412A GLN* 3.3 23.5 + - - +
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Residues in contact with ARG 409 (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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389A HIS* 4.0 25.3 + - + -
405A ALA 3.6 15.7 - - - +
406A LEU* 3.0 10.8 + - - +
408A SER* 1.3 80.3 + - - +
410A MET* 1.3 56.5 + - - +
412A GLN* 3.6 33.8 + - - +
413A HIS* 2.9 34.7 + - + -
552A LEU* 3.7 8.8 - - + +
592A GLU* 3.4 34.9 + - - +
594A ILE* 4.8 8.3 - - + -
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Residues in contact with MET 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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402A LEU* 3.9 16.2 - - + -
406A LEU* 2.5 41.5 + - + +
407A ILE* 2.9 11.8 + - - +
409A ARG* 1.3 74.2 - - - +
411A ARG* 1.3 61.4 + - - +
413A HIS* 2.9 21.0 + - - +
414A LEU* 3.1 16.3 + - + +
420A VAL* 4.3 10.8 - - + -
422A LEU* 4.1 17.5 - - + -
497A LEU* 6.1 0.4 - - + -
501A PHE* 3.6 20.4 - - + -
534A ILE* 3.4 36.8 - - + -
552A LEU* 3.7 22.0 - - + +
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Residues in contact with ARG 411 (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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407A ILE* 2.9 25.5 + - - +
408A SER* 3.3 21.1 - - - +
410A MET* 1.3 73.2 - - - +
412A GLN* 1.3 51.3 + - - +
414A LEU* 3.1 8.1 + - - +
415A GLN* 2.5 39.2 + - - +
500A LEU* 3.3 45.4 + - - +
501A PHE* 4.1 19.7 - - + -
502A PRO* 5.6 0.6 - - - +
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Residues in contact with GLN 412 (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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408A SER 3.3 15.9 + - - +
409A ARG* 3.6 37.8 + - - +
410A MET 3.2 0.8 - - - -
411A ARG* 1.3 78.2 - - - +
413A HIS* 1.3 61.3 + - + +
415A GLN* 3.3 22.0 - - + +
416A ALA* 4.1 5.0 + - - +
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Residues in contact with HIS 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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409A ARG* 2.9 30.1 - - + -
410A MET 2.9 9.2 + - - +
412A GLN* 1.3 80.1 - - + +
414A LEU* 1.3 62.7 + - + +
415A GLN 3.0 4.8 + - - -
416A ALA 3.6 3.5 + - - -
418A ASN* 3.1 38.5 + - + +
419A GLN 5.7 1.6 - - - +
420A VAL* 5.8 2.2 - - + -
551A THR* 2.7 34.6 + - - +
552A LEU* 3.6 21.7 - - + +
591A GLY* 5.7 1.3 - - - -
592A GLU* 2.9 44.3 + - + +
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Residues in contact with LEU 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 MET* 3.1 14.0 + - + +
411A ARG* 3.4 7.4 - - - +
413A HIS* 1.3 75.1 - - + +
415A GLN* 1.3 65.4 + - - +
416A ALA 3.4 0.4 - - - -
417A ASP* 3.2 13.1 + - - -
418A ASN 3.2 22.7 - - - +
420A VAL* 5.3 5.8 - - + -
501A PHE* 4.4 17.3 - - + -
504A VAL* 4.0 18.2 - - + -
532A ALA* 3.4 16.9 - - + +
533A ARG* 3.3 26.7 - - - +
534A ILE* 3.9 31.0 - - + -
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Residues in contact with GLN 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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411A ARG 2.5 20.9 + - - +
412A GLN* 3.3 18.8 - - + +
413A HIS 3.0 0.4 - - - -
414A LEU* 1.3 76.4 - - - +
416A ALA* 1.3 60.9 + - + +
417A ASP* 3.2 3.8 + - - +
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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
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412A GLN 4.1 5.1 + - - +
413A HIS 3.6 3.0 + - - +
414A LEU 3.4 0.2 - - - -
415A GLN* 1.3 78.9 - - + +
417A ASP* 1.3 65.7 + - - +
418A ASN* 2.9 27.9 - - - +
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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