Contacts of the helix formed by residues 450 - 458 (chain D) in PDB entry 5HJP
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 PRO 450 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272D THR* 3.5 38.8 - - + +
276D ILE* 3.7 24.5 - - + -
448D LYS 4.2 2.7 - - - +
449D LEU* 1.4 90.9 - - + +
451D PRO* 1.4 77.0 - - + +
452D LEU* 3.1 4.4 + - + +
453D LEU* 3.2 13.5 + - + -
454D SER* 3.1 15.8 + - - -
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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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449D LEU 3.7 0.9 - - - +
450D PRO* 1.4 85.8 - - + +
452D LEU* 1.3 56.7 + - - +
454D SER* 4.3 0.2 - - - -
455D GLU* 2.9 30.3 + - - +
463D SER* 3.7 19.1 - - - +
468D HIS* 3.6 35.9 - - + +
470D ILE* 3.5 10.6 - - + +
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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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276D ILE* 3.8 40.8 - - + +
279D VAL* 3.7 34.1 - - + -
280D GLN* 4.5 11.0 - - + +
450D PRO* 3.1 1.8 + - + +
451D PRO* 1.3 75.6 - - - +
453D LEU* 1.4 65.5 + - + +
455D GLU* 3.4 4.4 + - + +
456D ILE* 3.2 26.2 + - + +
470D ILE* 3.6 36.4 - - + +
471D LEU* 4.7 8.7 - - + +
474D LEU* 3.8 15.9 - - + -
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Residues in contact with LEU 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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272D THR* 4.0 14.6 - - - +
275D ALA* 4.1 9.0 - - + -
276D ILE* 4.2 16.6 - - + -
279D VAL* 4.0 25.8 - - + -
449D LEU* 3.9 12.6 - - + -
450D PRO* 3.2 27.5 + - + +
452D LEU* 1.4 72.4 - - + +
454D SER* 1.3 59.4 + - - +
456D ILE* 3.4 6.6 - - + +
457D TRP* 3.0 59.8 + - + +
501D 668 3.8 28.9 - - + -
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Residues in contact with SER 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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449D LEU* 4.1 3.0 - - - +
450D PRO 3.1 16.7 + - - -
451D PRO 3.7 4.7 - - - -
453D LEU* 1.3 73.6 - - - +
455D GLU* 1.4 55.8 + - - +
458D ASP* 2.8 29.5 + - - -
459D VAL* 3.0 18.7 + - - -
460D HIS* 3.0 45.3 + - - +
463D SER* 3.6 10.8 - - - -
464D GLY* 3.4 12.6 + - - -
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Residues in contact with GLU 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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301D ILE* 6.0 0.3 - - - +
305D LYS* 3.5 20.0 + - + +
451D PRO 2.9 17.8 + - - +
452D LEU* 3.6 6.5 - - + +
453D LEU 3.3 0.2 - - - -
454D SER* 1.4 78.8 - - - +
456D ILE* 1.3 64.2 + - + +
458D ASP* 3.3 9.4 + - - +
463D SER 3.3 20.4 + - - +
464D GLY* 4.3 1.9 - - - +
466D GLY* 4.0 19.0 + - - -
468D HIS* 4.1 2.4 - - - +
469D LYS* 3.4 11.4 + - - -
470D ILE* 3.0 35.2 + - - +
471D LEU* 3.0 35.6 + - + +
472D HIS* 4.6 1.7 + - - -
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Residues in contact with ILE 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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279D VAL* 3.7 19.3 - - + -
305D LYS* 3.4 37.9 - - + +
308D THR* 3.7 25.6 - - + +
452D LEU* 3.3 21.8 - - + +
453D LEU* 3.4 13.9 - - - +
455D GLU* 1.3 79.3 - - + +
457D TRP* 1.3 90.9 + - + +
458D ASP* 3.6 3.3 - - - +
471D LEU* 3.8 39.9 - - + -
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Residues in contact with TRP 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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305D LYS 4.6 6.9 + - - -
308D THR* 4.7 1.0 - - - +
309D ILE* 3.9 28.2 - - + +
312D MET* 3.6 37.7 - - + -
435D HIS* 3.4 28.3 - + + -
439D VAL* 4.9 7.8 - - + +
449D LEU* 3.9 13.5 - - + -
453D LEU* 3.0 50.9 + - + +
454D SER 3.7 0.2 - - - -
456D ILE* 1.3 100.2 - - + +
458D ASP* 1.4 71.9 + - - +
459D VAL* 3.5 12.1 + - + +
501D 668 3.4 35.7 - - + -
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Residues in contact with ASP 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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232B VAL* 5.2 1.0 - - - +
233B ALA* 5.8 4.9 - - + -
236B LEU* 3.3 23.9 - - + +
305D LYS* 2.9 31.0 + - - -
439D VAL* 5.6 0.5 - - - +
443D ARG* 4.3 4.7 + - - -
454D SER 2.8 14.4 + - - -
455D GLU 3.3 1.8 + - - +
456D ILE 4.2 2.6 - - - +
457D TRP* 1.4 77.4 - - - +
459D VAL* 1.3 57.9 + - - +
464D GLY 3.0 23.4 - - - +
465D SER* 4.9 2.9 - - - -
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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