Contacts of the helix formed by residues 448 - 465 (chain A) in PDB entry 3D0G
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 GLY 448 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A TYR* 4.1 16.5 + - - -
240A LEU* 4.6 4.0 - - - -
273A ARG 4.6 2.0 - - - -
275A TRP* 4.5 22.9 + - - -
443A ALA 2.8 17.7 + - - -
444A LEU 4.1 11.7 - - - -
445A THR 4.1 0.4 + - - -
446A ILE 3.5 0.4 - - - -
447A VAL* 1.3 75.0 - - - +
449A THR* 1.3 58.4 + - - +
450A LEU 3.4 0.5 + - - -
451A PRO* 3.5 10.2 - - - +
452A PHE* 4.4 6.9 + - - +
485A VAL* 5.8 1.0 - - - +
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Residues in contact with THR 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ARG* 2.3 40.4 + - - +
274A PHE* 3.3 18.9 - - + -
444A LEU 4.9 0.2 + - - -
445A THR 3.4 21.3 + - - +
446A ILE* 3.7 9.2 - - - +
447A VAL 3.0 1.4 + - - -
448A GLY* 1.3 75.2 - - - +
450A LEU* 1.3 66.1 + - + +
451A PRO 3.7 0.2 - - - -
452A PHE* 3.7 6.1 - - - +
453A THR* 2.6 44.8 + - - +
515A TYR* 5.3 5.4 - - + +
519A THR* 4.9 7.6 - - - +
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Residues in contact with LEU 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PHE* 4.6 2.7 - - + -
233A ILE* 4.6 19.1 - - + -
446A ILE 3.5 18.8 - - - +
447A VAL* 3.1 11.8 + - + +
449A THR* 1.3 78.9 - - + +
451A PRO* 1.3 70.3 - - + +
452A PHE 3.2 1.1 - - - -
453A THR* 3.8 2.2 - - - -
454A TYR* 2.9 30.3 + - - +
515A TYR 4.5 1.1 - - - +
516A TYR* 3.7 39.3 - - + +
519A THR* 3.8 31.6 - - + +
520A LEU* 4.5 2.5 - - + -
584A LEU* 3.8 28.9 - - + -
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Residues in contact with PRO 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PHE* 3.8 30.7 - - + -
233A ILE* 5.6 2.0 - - + -
237A TYR* 3.5 42.0 - - + -
447A VAL 3.4 13.2 - - - +
448A GLY 3.5 10.1 - - - +
450A LEU* 1.3 89.0 - - + +
452A PHE* 1.3 58.3 + - - +
454A TYR* 4.0 0.6 - - + +
455A MET* 2.9 33.4 + - - +
484A ILE* 4.1 16.8 - - - +
485A VAL* 3.7 7.5 - - + +
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Residues in contact with PHE 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A TRP* 3.7 32.3 - + + -
272A GLY 3.6 18.6 - - - +
273A ARG* 3.5 39.5 - - + -
448A GLY 4.4 5.1 + - - +
449A THR* 3.7 11.4 - - - +
450A LEU 3.2 0.6 - - - -
451A PRO* 1.3 80.6 - - - +
453A THR* 1.3 66.2 + - - +
455A MET* 3.6 3.0 - - - +
456A LEU* 3.0 39.3 + - + +
477A TRP* 6.0 0.9 - + - -
481A LYS* 4.1 26.2 - - - +
485A VAL* 4.2 18.9 - - + +
503A LEU* 4.9 9.9 - - + -
512A PHE* 3.8 19.1 - + - -
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Residues in contact with THR 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ARG* 5.4 0.3 + - - -
449A THR* 2.6 39.0 + - - +
450A LEU* 3.8 5.6 - - - -
452A PHE* 1.3 75.4 - - - +
454A TYR* 1.3 67.4 + - - +
456A LEU* 3.4 4.3 + - - +
457A GLU* 3.3 17.8 + - - +
512A PHE* 3.3 50.6 - - + +
513A ILE* 4.6 2.2 - - - +
515A TYR* 4.0 8.0 - - + +
516A TYR* 4.0 26.7 - - + +
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Residues in contact with TYR 454 (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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226A VAL* 4.1 18.6 - - + -
227A GLU* 2.9 39.4 + - + +
230A PHE* 3.7 41.7 - + + -
450A LEU 2.9 17.5 + - - +
451A PRO* 4.0 3.1 - - + +
453A THR* 1.3 77.6 - - - +
455A MET* 1.3 66.5 + - - +
457A GLU* 3.2 1.9 + - - +
458A LYS* 2.8 54.5 + - + +
461A TRP* 4.9 7.6 - + - -
484A ILE* 4.0 22.1 - - + +
513A ILE* 4.5 11.4 - - + -
516A TYR* 4.4 14.3 - - + -
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Residues in contact with MET 455 (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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451A PRO 2.9 20.5 + - - +
452A PHE 3.6 2.5 - - - +
454A TYR* 1.3 77.4 - - - +
456A LEU* 1.3 64.2 + - - +
458A LYS* 2.9 18.4 + - - +
459A TRP* 2.9 19.9 + - + -
477A TRP* 3.3 37.9 - - + +
480A MET* 3.8 26.9 - - + +
481A LYS* 3.5 40.6 - - - -
484A ILE* 3.9 15.3 - - + -
485A VAL* 3.5 15.7 - - + -
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Residues in contact with LEU 456 (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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452A PHE* 3.0 31.5 + - + +
453A THR 3.5 5.4 - - - +
455A MET* 1.3 85.8 - - - +
457A GLU* 1.3 58.9 + - - +
459A TRP* 3.5 3.6 + - - +
460A ARG* 3.0 60.1 + - - +
477A TRP* 3.4 27.6 - - + -
500A PRO* 4.8 2.7 - - + +
503A LEU* 4.8 7.2 - - + -
506A VAL* 3.9 19.7 - - + -
512A PHE* 3.6 26.2 - - + -
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Residues in contact with GLU 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TRP* 4.0 12.5 - - - +
453A THR 3.3 5.0 + - - +
454A TYR 3.2 7.3 + - - +
456A LEU* 1.3 75.8 - - - +
458A LYS* 1.3 58.2 + - - +
460A ARG* 2.2 40.4 + - - +
461A TRP* 2.6 70.5 + - + -
511A SER* 4.5 1.9 - - - -
512A PHE* 3.4 14.2 + - + -
513A ILE* 3.3 54.2 + - + +
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Residues in contact with LYS 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ILE* 4.9 6.7 - - - +
227A GLU* 3.0 22.6 + - - +
454A TYR* 2.8 46.4 + - + +
455A MET* 2.9 11.4 + - - +
457A GLU* 1.3 76.1 - - - +
459A TRP* 1.3 62.5 + - - +
461A TRP* 3.7 17.7 - - + +
462A MET* 3.1 53.7 + - - +
467A GLU* 5.2 2.2 + - - -
480A MET* 3.4 19.7 - - + -
484A ILE* 5.5 3.4 - - + -
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Residues in contact with TRP 459 (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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180A TYR* 4.2 29.6 - + - -
455A MET* 2.9 21.5 + - + -
456A LEU 3.6 7.4 - - - +
458A LYS* 1.3 75.3 - - - +
460A ARG* 1.3 87.0 + - + +
462A MET* 3.0 4.7 + - - +
463A VAL* 2.8 49.8 + - + +
468A ILE* 4.1 18.1 - - + +
473A TRP* 3.1 51.0 + + + +
474A MET* 5.3 1.3 - - - -
476A LYS* 4.4 2.4 - - - +
477A TRP* 3.4 43.1 - + + +
480A MET* 3.5 11.3 - - + +
498A CYS* 5.2 0.9 - - - -
500A PRO* 3.4 30.5 - - + -
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Residues in contact with ARG 460 (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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180A TYR* 3.8 17.7 + - - +
183A TYR* 5.9 0.2 + - - -
203A TRP* 3.5 15.1 - - + -
456A LEU* 3.0 35.3 + - - +
457A GLU* 2.2 49.8 + - - +
459A TRP* 1.3 93.3 - - + +
461A TRP* 1.3 65.5 + - + +
463A VAL* 3.2 3.8 + - - +
464A PHE* 3.1 50.4 + - + -
505A HIS 3.5 15.2 + - - -
506A VAL* 3.8 20.6 + - - +
510A TYR 2.5 31.9 + - - -
512A PHE* 3.4 8.1 - - - +
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Residues in contact with TRP 461 (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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198A ASP* 4.7 1.7 - - - +
200A GLY* 4.1 12.4 + - - -
203A TRP* 5.2 7.8 - + - +
204A ARG* 3.1 36.2 + - + +
222A LEU* 4.1 24.0 - - + -
223A ILE* 3.8 46.0 - - + -
226A VAL* 4.9 4.5 - - + -
454A TYR* 4.9 13.9 - + - -
457A GLU* 2.6 55.7 + - + +
458A LYS* 3.7 17.5 - - + +
460A ARG* 1.3 73.6 - - + +
462A MET* 1.3 63.1 + - + +
464A PHE* 3.1 17.3 + + - +
465A LYS* 3.2 19.9 + - + +
513A ILE* 4.2 26.7 - - + +
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Residues in contact with MET 462 (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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458A LYS* 3.1 44.5 + - - +
459A TRP 3.0 1.2 + - - -
461A TRP* 1.3 72.7 - - + +
463A VAL* 1.3 65.5 + - - +
465A LYS* 3.3 8.6 + - - +
467A GLU* 3.1 57.8 + - + +
468A ILE* 3.2 36.9 + - + -
476A LYS* 4.3 18.4 - - - -
480A MET* 4.0 21.5 - - - -
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Residues in contact with VAL 463 (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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180A TYR* 5.3 0.9 - - + -
184A VAL* 4.0 22.1 - - + +
188A ASN* 4.7 0.7 + - - -
459A TRP* 2.8 57.8 + - + +
460A ARG* 3.5 9.6 - - - +
462A MET* 1.3 76.0 - - - +
464A PHE* 1.3 65.8 + - + +
466A GLY* 3.4 12.3 + - - -
468A ILE* 4.3 14.1 - - + +
473A TRP* 3.7 39.9 - - + +
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Residues in contact with PHE 464 (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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180A TYR* 4.1 11.4 - - - -
183A TYR* 4.2 12.6 - + - -
184A VAL* 3.6 40.6 - - + -
187A LYS* 5.6 0.2 - - + -
188A ASN* 3.0 29.9 + - - +
192A ARG* 4.4 4.2 + - - -
198A ASP* 3.1 15.6 - - + +
199A TYR* 3.9 27.6 - + + -
200A GLY* 3.7 34.3 - - - +
203A TRP* 4.2 11.4 - + - -
460A ARG* 3.1 43.1 + - + -
461A TRP* 3.1 7.3 + + - +
463A VAL* 1.3 82.4 - - + +
465A LYS* 1.3 58.6 + - - +
466A GLY 3.3 0.4 + - - -
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Residues in contact with LYS 465 (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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192A ARG* 5.9 3.0 + - - +
197A GLU* 4.5 12.3 + - - +
198A ASP* 3.0 28.3 - - - +
204A ARG* 4.9 9.0 - - - +
223A ILE* 5.9 6.0 - - - +
461A TRP* 3.2 15.7 + - - +
462A MET* 3.3 9.6 + - - +
464A PHE* 1.3 75.9 - - - +
466A GLY* 1.3 57.7 + - - +
467A GLU* 2.7 44.1 + - + +
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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
------------------------------------------------------------
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