Contacts of the helix formed by residues 448 - 463 (chain D) in PDB entry 5I94
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 448 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296D VAL 4.6 0.5 + - - -
297D ASN* 3.0 25.2 + - - -
445D ARG* 4.0 13.5 - - - +
447D LEU* 1.3 76.1 - - - +
449D PRO* 1.3 70.8 - - - +
450D GLU* 3.7 12.0 + - - +
451D ALA* 3.0 35.2 + - - +
452D VAL* 3.0 12.4 + - - +
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Residues in contact with PRO 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530C ASP* 6.1 0.4 - - - +
534C HIS* 4.4 15.9 - - + +
535C PHE* 5.2 1.8 - - - -
536C ALA* 4.1 31.4 - - + +
436D GLY* 4.3 16.4 - - - +
445D ARG* 4.1 21.1 - - - +
447D LEU 3.9 0.8 - - - +
448D SER* 1.3 88.2 - - - +
450D GLU* 1.3 59.0 + - + +
451D ALA 3.2 0.2 - - - -
452D VAL* 3.7 4.8 - - + +
453D ARG* 2.8 39.1 + - - +
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Residues in contact with GLU 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D VAL* 4.2 6.8 - - - +
300D GLY* 3.9 9.4 - - - -
301D THR* 2.6 47.5 + - - +
448D SER* 3.1 9.1 + - - +
449D PRO* 1.3 82.6 - - + +
451D ALA* 1.3 58.6 + - - +
453D ARG* 3.6 25.5 - - - +
454D ASN* 3.0 34.0 + - - +
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Residues in contact with ALA 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D TYR* 4.8 0.2 - - - -
293D ALA* 3.5 29.8 - - + +
296D VAL* 3.6 18.1 - - + +
297D ASN* 3.9 6.7 - - + +
447D LEU* 4.6 5.6 - - + -
448D SER* 3.0 23.4 + - - +
450D GLU* 1.3 76.5 - - - +
452D VAL* 1.3 65.4 + - - +
454D ASN* 3.3 1.9 + - - +
455D THR* 2.8 30.8 + - - -
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Residues in contact with VAL 452 (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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529C TYR 5.5 1.3 - - - +
433D LEU* 3.2 41.2 - - + +
436D GLY* 3.9 16.8 - - - -
437D GLY* 3.5 26.7 - - - +
447D LEU* 3.7 19.5 - - + -
448D SER 3.0 16.4 + - - +
449D PRO* 3.9 4.5 - - + +
451D ALA* 1.3 76.8 - - - +
453D ARG* 1.3 64.0 + - - +
455D THR* 3.5 3.2 + - - -
456D LEU* 3.2 29.8 + - + +
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Residues in contact with ARG 453 (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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473C PHE 5.7 0.8 + - - -
527C HIS* 3.6 38.3 + - + +
529C TYR* 3.4 25.9 - - - +
530C ASP* 3.2 26.0 + - - +
538C LYS* 4.1 17.1 - - - +
449D PRO* 2.8 28.0 + - - +
450D GLU* 3.6 32.7 - - - +
452D VAL* 1.3 79.1 - - - +
454D ASN* 1.3 71.6 + - - +
456D LEU* 3.5 2.3 + - - +
457D SER* 3.0 26.2 + - - +
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Residues in contact with ASN 454 (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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473C PHE* 3.6 19.1 - - + +
292D TYR* 3.3 25.7 + - + +
296D VAL* 3.9 8.9 - - + +
301D THR* 2.7 39.6 + - - +
450D GLU 3.0 19.7 + - - +
451D ALA* 3.8 4.5 - - - +
452D VAL 3.3 0.2 - - - -
453D ARG* 1.3 94.9 + - - +
455D THR* 1.3 61.6 + - - +
457D SER* 3.3 19.0 - - - -
458D LEU* 3.4 16.3 + - - +
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Residues in contact with THR 455 (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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289D PRO* 3.5 42.2 - - + +
292D TYR* 3.5 21.2 - - + -
293D ALA* 3.6 14.3 - - + +
332D MET* 4.6 1.6 - - + -
433D LEU* 4.9 10.5 - - + -
451D ALA 2.8 21.8 + - - -
452D VAL* 4.0 4.9 - - - -
454D ASN* 1.3 74.2 - - - +
456D LEU* 1.3 62.0 + - - +
457D SER 3.0 1.1 - - - -
458D LEU* 3.0 3.3 + - - +
459D MET* 2.8 37.0 + - + +
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Residues in contact with LEU 456 (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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529C TYR* 3.6 45.2 - - + +
433D LEU* 3.8 35.0 - - + +
452D VAL* 3.2 19.8 + - + +
455D THR* 1.3 78.3 - - - +
457D SER* 1.3 62.5 + - - +
459D MET* 4.3 10.3 - - - -
460D HIS* 3.1 22.9 + - - +
478D PRO* 3.9 12.7 - - + +
490D VAL* 3.8 36.1 - - + -
492D PRO* 4.3 10.5 - - + -
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Residues in contact with SER 457 (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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472C ALA 4.7 2.6 + - - -
473C PHE* 4.2 25.5 + - - -
527C HIS* 3.5 26.5 + - - -
529C TYR* 3.8 9.7 - - - -
453D ARG 3.0 15.7 + - - -
454D ASN* 3.3 13.3 - - - -
455D THR 3.0 0.6 - - - -
456D LEU* 1.3 77.2 - - - +
458D LEU* 1.3 59.6 + - - +
460D HIS* 3.1 21.8 + - - +
461D SER* 3.6 9.0 + - - -
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Residues in contact with LEU 458 (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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473C PHE* 3.8 18.8 - - + -
292D TYR* 3.6 29.2 - - + +
305D HIS* 4.3 4.3 - - + -
310D LYS* 3.4 31.6 - - - +
330D ASN* 5.1 0.2 - - + -
331D PRO* 3.6 31.0 - - + -
332D MET* 3.7 20.1 - - + +
454D ASN 3.4 10.1 + - - +
455D THR 3.0 2.2 + - - +
457D SER* 1.3 75.7 - - - +
459D MET* 1.3 62.3 + - - +
460D HIS 3.0 1.6 - - - -
461D SER* 4.2 8.1 - - - +
462D CYS* 2.9 41.9 + - - +
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Residues in contact with MET 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D PRO* 3.8 24.5 - - + -
332D MET* 3.9 6.5 - - + +
433D LEU* 4.4 7.2 - - + -
455D THR* 2.8 35.8 + - + +
456D LEU* 4.3 13.0 - - - -
458D LEU* 1.3 77.8 - - - +
460D HIS* 1.3 61.7 + - - +
463D GLY* 3.3 19.4 + - - -
464D MET* 5.6 1.2 - - - +
471D PHE* 6.1 0.9 - - - -
477D LEU 5.1 0.2 - - - +
478D PRO* 3.9 17.3 - - + +
479D ALA* 3.4 47.3 + - - +
480D LYS* 4.0 7.0 - - + +
488D LEU* 3.8 19.3 - - + +
490D VAL* 4.4 13.0 - - + -
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Residues in contact with HIS 460 (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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460C HIS* 3.3 38.4 + + - -
529C TYR* 2.5 32.1 + + + +
456D LEU 3.1 13.3 + - - +
457D SER 3.1 15.5 - - - +
458D LEU 3.0 0.4 - - - -
459D MET* 1.3 78.3 - - - +
461D SER* 1.3 63.7 + - - +
468D SER* 4.4 2.4 - - - +
471D PHE* 5.7 1.9 - - - -
472D ALA* 3.5 43.2 + - + +
476D GLY* 4.6 13.1 + - - -
477D LEU 4.7 5.2 + - - +
478D PRO* 4.2 7.6 - - - -
528D ASN* 3.7 14.6 - - + -
529D TYR* 5.2 4.9 - + - -
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Residues in contact with SER 461 (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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460C HIS* 5.9 1.1 - - - -
461C SER* 6.4 2.0 - - - -
310D LYS 5.5 0.2 + - - -
312D PRO* 3.5 33.5 - - - +
457D SER 3.7 11.7 + - - -
458D LEU* 3.3 4.9 + - - +
460D HIS* 1.3 87.2 - - - +
462D CYS* 1.3 74.1 + - - +
463D GLY 3.8 0.9 - - - -
468D SER* 3.4 20.3 - - - -
469D GLY* 5.8 0.2 - - - -
472D ALA* 5.2 2.2 - - - -
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Residues in contact with CYS 462 (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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311D GLU 4.1 2.2 - - - -
312D PRO* 3.7 15.9 - - + -
330D ASN* 3.4 35.7 - - - +
332D MET* 3.2 30.3 - - + +
333D VAL* 5.7 2.1 - - + +
458D LEU* 2.9 19.9 + - - +
461D SER* 1.3 96.9 - - - +
463D GLY* 1.3 61.8 + - - +
464D MET 3.8 0.2 + - - -
465D TYR* 4.4 5.1 + - - -
468D SER* 3.2 12.2 + - - -
480D LYS* 4.7 0.7 - - - -
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Residues in contact with GLY 463 (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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332D MET* 5.0 0.2 - - - -
459D MET* 3.3 13.7 + - - -
460D HIS 5.0 0.4 - - - -
462D CYS* 1.3 80.7 - - - +
464D MET* 1.3 63.4 + - - +
465D TYR 3.4 2.5 + - - -
468D SER* 3.2 2.2 + - - -
479D ALA 3.3 21.1 - - - -
480D LYS* 3.2 31.6 + - - +
481D SER* 3.4 11.6 + - - -
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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