Contacts of the helix formed by residues 450 - 458 (chain D) in PDB entry 5NSS
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 HIS 450 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358D GLY 3.9 6.7 + - - -
359D PRO 4.7 4.2 + - - -
360D TYR 5.1 2.0 + - - -
361D LEU* 6.1 2.6 - - + +
362D ARG 4.4 7.0 + - - +
363D LEU* 3.4 56.8 - - + +
365D GLN 5.5 4.2 + - - +
437D PHE* 5.4 1.5 - - + -
449D LEU* 1.3 76.4 - - + +
451D PRO* 1.3 65.8 - - + +
452D LEU* 3.3 39.7 - - + +
453D VAL* 3.0 20.9 + - + +
454D CYS* 2.9 24.9 + - - -
622D ASP* 4.7 4.7 - - - -
625D MET* 3.3 32.1 - - + +
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Residues in contact with PRO 451 (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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809C GLY 5.3 1.1 - - - +
812C PHE* 3.8 36.6 - - + -
357D VAL* 3.7 18.6 - - + -
358D GLY 3.4 16.6 - - - +
359D PRO* 5.0 0.4 - - + -
449D LEU 3.3 3.3 - - - +
450D HIS* 1.3 91.2 - - - +
452D LEU* 1.3 66.5 + - + +
454D CYS* 3.0 26.9 + - + +
455D ALA* 3.3 7.3 + - - +
501D VAL 5.5 0.3 - - - +
625D MET* 3.5 23.3 - - + -
629D PHE* 4.7 9.0 - - + -
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Residues in contact with LEU 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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812C PHE* 6.4 1.6 - - + -
363D LEU* 4.5 7.0 - - + -
450D HIS* 3.3 25.9 - - + +
451D PRO* 1.3 79.8 - - + +
453D VAL* 1.3 60.8 + - - +
455D ALA* 3.8 6.2 + - - +
456D ALA* 3.7 13.9 + - - +
500D ILE* 4.7 16.9 - - + -
501D VAL 3.2 35.8 + - - +
502D PRO* 3.7 19.1 - - + -
506D VAL* 5.3 6.1 - - + -
622D ASP* 4.5 11.9 - - - +
625D MET* 3.9 26.5 - - + -
629D PHE* 5.8 1.8 - - + -
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Residues in contact with VAL 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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363D LEU* 3.7 27.1 - - + +
435D GLN* 3.2 24.0 - - - +
437D PHE* 3.6 11.7 - - + -
449D LEU* 4.6 1.1 - - + -
450D HIS* 3.0 32.1 + - + +
452D LEU* 1.3 75.6 - - - +
454D CYS* 1.3 60.8 + - - +
455D ALA 3.2 0.7 - - - -
456D ALA* 2.9 23.1 + - + +
457D TYR* 2.9 36.5 + - + -
486D SER* 4.3 4.9 - - - -
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Residues in contact with CYS 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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812C PHE* 4.7 6.1 - - + -
813C GLU* 5.7 1.3 - - - +
355D ILE* 4.4 0.2 - - - -
449D LEU* 3.6 27.4 - - - -
450D HIS 2.9 24.6 + - - -
451D PRO* 3.0 15.7 + - + +
453D VAL* 1.3 77.3 - - - +
455D ALA* 1.3 56.5 + - - +
457D TYR* 3.3 8.6 + - - +
458D ASN* 2.9 23.6 + - - -
459D ALA* 3.2 24.2 + - + +
461D PHE* 3.6 34.3 - - + -
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Residues in contact with ALA 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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812C PHE* 5.6 6.8 - - + -
813C GLU* 5.9 3.6 - - - +
451D PRO 3.3 7.6 + - - +
452D LEU 4.0 7.0 - - - +
453D VAL 3.2 0.4 - - - -
454D CYS* 1.3 77.7 - - - +
456D ALA* 1.3 61.7 + - - +
458D ASN* 3.3 14.3 + - - +
459D ALA 5.5 0.2 - - - -
499D ILE* 5.9 2.4 - - - +
501D VAL* 3.6 31.2 - - + +
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Residues in contact with ALA 456 (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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430D HIS* 3.1 32.4 + - + -
432D LEU* 5.3 10.8 - - + -
435D GLN* 4.8 13.2 - - - +
452D LEU 3.7 4.2 + - - +
453D VAL* 2.9 22.8 + - + +
455D ALA* 1.3 80.6 - - - +
457D TYR* 1.3 62.7 + - + +
458D ASN* 3.4 0.9 + - - +
499D ILE* 5.6 17.5 - - + +
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Residues in contact with TYR 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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423D LEU* 3.9 15.5 - - + +
425D ARG* 4.4 21.0 - - + +
427D PRO 5.7 0.7 - - - +
430D HIS* 5.2 3.0 + - - -
432D LEU 3.3 19.5 - - - -
433D GLY* 3.1 31.8 - - - -
435D GLN* 3.2 34.5 + - + +
437D PHE* 3.4 13.0 - + - -
449D LEU* 3.8 32.5 - - + -
453D VAL* 2.9 31.3 + - + -
454D CYS* 3.8 6.5 - - - +
456D ALA* 1.3 76.2 - - - +
458D ASN* 1.3 62.9 + - - +
459D ALA* 3.0 18.9 + - + +
466D MET* 5.0 7.4 - - + -
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Residues in contact with ASN 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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425D ARG* 3.3 14.7 + - - +
429D LEU* 5.0 15.9 - - + +
430D HIS* 5.9 1.8 - - - +
454D CYS 2.9 7.9 + - - -
455D ALA* 3.3 11.0 + - - +
456D ALA 3.2 5.3 - - - +
457D TYR* 1.3 77.2 - - - +
459D ALA* 1.3 65.3 + - - +
460D ASP* 3.5 11.1 - - - +
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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