Contacts of the helix formed by residues 406 - 418 (chain D) in PDB entry 2DB3
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402D ASP 3.3 15.8 + - - +
403D ARG* 3.4 28.6 + - - +
405D LEU* 1.3 77.9 - - - +
407D MET* 1.3 100.1 + - - +
408D GLY 3.2 4.6 + - - +
409D PHE 3.2 2.8 + - - -
410D SER* 2.9 21.3 + - - -
439D ILE* 4.1 19.4 - - + +
442D MET* 4.7 4.1 - - - +
569D LYS* 4.2 17.2 + - - +
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Residues in contact with MET 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D ASP* 1.3 94.9 + - - +
408D GLY* 1.3 65.3 + - - +
409D PHE 3.3 0.7 + - - -
410D SER* 3.7 15.6 + - - -
411D GLU* 4.8 2.9 + - - +
442D MET* 5.7 0.4 - - - +
569D LYS* 4.2 21.1 - - - +
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Residues in contact with GLY 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403D ARG* 5.9 6.0 - - - -
406D ASP* 3.2 4.2 + - - +
407D MET* 1.3 79.7 - - - +
409D PHE* 1.3 66.4 + - - +
411D GLU* 5.2 2.1 + - - +
4H U 5.6 6.3 - - - -
5H U 5.6 2.4 - - - +
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Residues in contact with PHE 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D PRO* 3.5 37.2 - - + -
376D PRO* 3.5 32.5 - - + -
403D ARG* 3.7 27.1 + - + +
404D MET* 3.2 29.8 - - + +
406D ASP 3.2 3.2 + - - -
408D GLY* 1.3 78.7 - - - +
410D SER* 1.3 65.4 + - - +
411D GLU 3.2 3.8 + - - -
412D ASP* 3.2 10.0 + - + +
413D MET* 3.0 22.4 + - + +
4H U 3.6 18.2 - - - -
5H U 3.4 40.2 - - - -
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Residues in contact with SER 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404D MET 3.6 7.1 + - - -
405D LEU* 3.7 16.8 - - - +
406D ASP 2.9 17.1 + - - -
407D MET* 3.7 12.3 + - - -
409D PHE* 1.3 75.7 - - - +
411D GLU* 1.3 63.1 + - - +
413D MET* 3.7 3.3 - - - +
414D ARG* 2.8 33.3 + - - +
442D MET* 5.8 3.4 - - - -
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Residues in contact with GLU 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407D MET 4.8 3.4 + - - +
408D GLY 5.2 1.8 + - - +
409D PHE 3.2 1.6 + - - -
410D SER* 1.3 83.2 + - - +
412D ASP* 1.3 65.3 + - - +
414D ARG* 3.6 6.8 - - - +
415D ARG* 3.0 33.3 + - + +
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Residues in contact with ASP 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376D PRO* 4.1 21.0 - - + +
377D GLY* 4.5 7.8 + - - -
380D LEU* 3.2 29.1 - - + +
409D PHE* 3.2 11.6 + - + +
411D GLU* 1.3 82.2 - - - +
413D MET* 1.3 65.1 + - - +
415D ARG* 3.3 15.0 + - - +
416D ILE* 3.0 30.6 + - - +
5H U 4.8 4.2 + - - +
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Residues in contact with MET 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D VAL* 4.1 12.8 - - + -
376D PRO* 3.6 18.6 - - + -
398D LEU* 3.6 35.0 - - + -
404D MET* 3.4 47.6 - - + +
405D LEU* 4.4 4.3 - - + -
409D PHE* 3.0 19.8 + - + +
410D SER* 3.7 4.5 - - - +
412D ASP* 1.3 74.8 - - - +
414D ARG* 1.3 67.1 + - - +
416D ILE* 3.1 8.9 + - + +
417D MET* 2.9 50.8 + - + +
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Residues in contact with ARG 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410D SER 2.8 17.8 + - - +
411D GLU* 3.6 6.5 - - - +
413D MET* 1.3 77.0 - - - +
415D ARG* 1.3 57.3 + - + +
417D MET* 4.4 8.7 - - - +
418D THR* 2.8 53.3 + - + +
445D GLU* 3.0 40.4 + - - -
446D PHE* 3.8 20.5 - - + -
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Residues in contact with ARG 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D LEU* 3.6 32.1 - - + +
383D VAL* 5.3 2.4 - - - +
384D ASP* 2.6 42.0 + - - -
411D GLU* 3.0 21.2 + - + +
412D ASP* 3.5 21.4 + - - +
414D ARG* 1.3 77.7 - - + +
416D ILE* 1.3 60.1 + - - +
418D THR* 4.0 3.8 - - - -
419D HIS* 3.3 33.6 + - - +
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Residues in contact with ILE 416 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322D VAL* 5.1 6.3 - - + -
324D VAL* 4.8 7.0 - - + -
376D PRO* 4.4 14.8 - - + -
379D LEU* 4.0 20.2 - - + -
380D LEU* 3.1 32.3 - - + -
390D PHE* 4.0 30.3 - - + -
396D VAL* 5.9 5.2 - - + -
412D ASP 3.0 21.6 + - - +
413D MET* 3.6 18.6 - - + +
414D ARG 3.1 0.2 - - - -
415D ARG* 1.3 76.4 - - - +
417D MET* 1.3 67.5 + - + +
418D THR 3.1 5.3 + - - -
419D HIS* 3.2 18.0 + - - +
422D MET* 4.5 5.9 - - - +
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Residues in contact with MET 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396D VAL* 4.4 21.3 - - + -
398D LEU* 4.1 24.2 - - + -
405D LEU* 4.1 7.2 - - + -
413D MET* 2.9 37.8 + - + +
414D ARG 4.4 0.7 - - - +
416D ILE* 1.3 79.6 - - + +
418D THR* 1.3 60.0 + - - +
419D HIS 3.5 0.2 - - - -
422D MET* 3.9 22.5 - - - +
426D HIS* 4.8 9.0 + - + -
428D THR* 5.0 3.6 - - - -
430D MET* 4.9 3.8 - - - -
446D PHE* 3.6 58.4 - - + -
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Residues in contact with THR 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414D ARG* 2.8 34.2 + - + +
415D ARG* 4.0 4.0 - - - -
417D MET* 1.3 81.0 + - - +
419D HIS* 1.3 65.2 + - - +
420D VAL* 3.5 3.1 + - - +
422D MET* 5.0 0.4 - - - -
446D PHE* 4.2 17.2 - - - -
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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
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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