Contacts of the helix formed by residues 450 - 459 (chain D) in PDB entry 5LS6
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 ASN 450 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317D ASN* 4.2 25.4 + - - +
325D TYR* 5.8 0.9 - - - -
447D TYR* 3.5 26.0 + - + +
448D TYR 2.9 5.8 + - - +
449D ASP* 1.3 72.1 - - - +
451D PHE* 1.3 62.2 + - - +
452D CYS* 3.6 19.8 - - - +
453D ALA* 3.0 27.0 + - - +
454D ILE* 3.1 13.9 + - - +
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Residues in contact with PHE 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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325D TYR* 3.6 25.5 - + + -
335D ALA* 3.8 17.9 - - + -
440D PHE* 5.1 1.1 - + - -
444D ILE* 5.0 6.5 - - + -
449D ASP* 2.9 46.7 + - + -
450D ASN* 1.3 71.0 - - - +
452D CYS* 1.3 56.2 + - - +
454D ILE* 3.8 6.9 - - + +
455D ALA* 2.9 34.1 + - - +
463D CYS* 4.0 15.9 - - - +
466D VAL* 3.6 32.8 - - + +
467D TYR* 3.8 24.0 - + + -
470D ARG* 3.5 39.0 - - + -
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Residues in contact with CYS 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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317D ASN* 4.9 14.6 - - - +
319D PRO 4.8 3.8 - - - -
320D CYS* 3.5 20.9 - - - -
324D CYS* 4.3 2.0 - - - -
325D TYR* 4.1 15.0 - - - -
450D ASN* 3.6 12.8 - - - +
451D PHE* 1.3 77.9 - - - +
453D ALA* 1.3 60.6 + - - +
455D ALA* 4.1 2.1 + - - +
456D ARG* 3.5 20.4 + - - +
463D CYS* 3.7 3.5 - - - -
802D ZN 2.1 39.7 - - - -
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Residues in contact with ALA 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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447D TYR* 3.7 27.6 - - + -
450D ASN* 3.0 26.7 + - - +
452D CYS* 1.3 76.6 - - - +
454D ILE* 1.3 56.2 + - - +
456D ARG* 3.0 13.0 + - - +
457D LEU* 2.8 41.8 + - + +
675F ASP* 6.1 2.0 - - + -
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Residues in contact with ILE 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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440D PHE* 3.8 9.4 - - + -
443D LEU* 3.7 34.7 - - + +
444D ILE* 4.4 9.2 - - + +
447D TYR* 3.3 30.3 - - + -
448D TYR 4.8 0.7 - - - +
449D ASP 4.9 2.2 - - - +
450D ASN 3.1 34.2 + - - +
451D PHE* 3.3 9.5 + - + +
453D ALA* 1.3 77.8 - - - +
455D ALA* 1.3 51.9 + - - +
457D LEU* 3.3 0.9 + - - +
458D ILE* 2.7 64.6 + - + +
466D VAL* 3.4 22.9 - - + -
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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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320D CYS* 5.8 0.9 - - - -
451D PHE 2.9 15.3 + - - +
452D CYS 4.2 3.6 - - - +
454D ILE* 1.3 76.4 - - - +
456D ARG* 1.3 55.1 + - - +
458D ILE* 3.3 2.4 + - - +
459D GLY* 2.7 32.9 + - - -
461D LYS 3.5 15.3 - - - +
462D THR* 3.4 9.4 - - - -
463D CYS* 3.2 31.9 - - + +
466D VAL* 3.5 10.7 - - + +
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Residues in contact with ARG 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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452D CYS 3.5 14.7 + - - +
453D ALA* 3.0 14.0 + - - +
455D ALA* 1.3 78.3 - - - +
457D LEU* 1.3 53.4 + - + +
459D GLY* 3.5 5.8 + - - -
675F ASP* 3.2 35.5 + - - +
679F THR* 3.9 20.9 + - - +
682F ARG* 2.7 28.8 + - - +
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Residues in contact with LEU 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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443D LEU* 3.8 16.6 - - + -
447D TYR* 3.4 35.4 - - + +
453D ALA* 2.8 25.1 + - + +
454D ILE 4.0 2.7 - - - +
456D ARG* 1.3 73.9 - - + +
458D ILE* 1.3 65.9 + - - +
459D GLY 3.1 1.1 - - - -
657F MET* 3.5 26.8 - - - +
674F ILE* 3.5 24.9 - - + +
675F ASP* 3.0 38.6 - - + +
678F VAL* 4.9 5.2 - - + -
682F ARG* 3.1 22.5 + - - +
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Residues in contact with ILE 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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432D TRP* 3.9 27.6 - - + -
436D GLU* 4.2 18.8 - - + +
439D MET* 4.7 13.2 - - + -
440D PHE* 4.0 11.9 - - + +
443D LEU* 4.0 12.8 - - + -
454D ILE* 2.7 47.7 + - + +
455D ALA* 3.9 3.4 - - - +
457D LEU* 1.3 73.5 - - - +
459D GLY* 1.3 58.1 + - - +
460D THR* 3.0 35.8 + - + +
461D LYS* 4.4 9.6 - - + +
466D VAL* 4.2 4.9 - - + -
654F ARG* 5.8 1.4 + - - -
657F MET* 5.5 0.2 - - - -
682F ARG* 4.2 4.2 + - - -
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Residues in contact with GLY 459 (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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455D ALA 2.7 16.5 + - - -
456D ARG* 3.5 12.1 - - - -
457D LEU 3.1 1.5 - - - -
458D ILE* 1.3 73.8 - - - +
460D THR* 1.3 56.7 + - - +
461D LYS 3.5 4.2 + - - -
682F ARG* 4.1 11.0 - - - -
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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