Contacts of the helix formed by residues 458 - 468 (chain D) in PDB entry 4K9P
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 TYR 458 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B ASN* 3.4 19.3 + - - -
24B PRO* 4.3 8.7 - - + -
43B LEU* 4.5 3.9 - - + +
45B LEU* 4.2 10.7 + - - +
429D GLY* 3.8 27.2 + - - -
433D TYR* 4.1 5.1 + - - -
457D THR* 1.3 80.9 + - - +
459D GLY* 1.3 66.3 + - - +
460D ILE 3.3 2.0 - - - -
461D LEU* 2.7 39.7 + - + -
462D ARG* 3.1 7.8 + - - +
475D GLY 3.4 26.2 - - - -
476D LEU* 2.9 15.9 + - - +
478D VAL* 3.7 25.5 - - + +
602D TPP 3.3 44.9 - - + -
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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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378D SER* 4.1 11.2 - - - -
455D ASN* 4.7 4.3 - - - -
457D THR* 3.1 13.9 + - - -
458D TYR* 1.3 70.9 - - - +
460D ILE* 1.3 63.4 + - - -
462D ARG* 2.9 18.1 + - - +
463D TRP* 3.1 12.1 + - - +
602D TPP 3.0 20.0 + - - -
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Residues in contact with ILE 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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281D TYR* 5.6 7.4 - - + +
377D THR* 3.1 34.5 - - - +
378D SER* 3.7 10.7 - - - -
458D TYR 3.0 0.4 + - - -
459D GLY* 1.3 70.7 - - - -
461D LEU* 1.3 73.9 + - + +
463D TRP* 3.1 14.0 + - + +
464D PHE* 3.0 42.0 + - + -
602D TPP 2.7 52.2 + - + +
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Residues in contact with LEU 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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24B PRO* 3.7 13.5 - - + +
25B GLY* 3.8 5.6 - - - -
26B SER* 3.7 34.5 - - - +
29B LEU* 3.8 8.5 - - + +
458D TYR* 2.7 37.4 + - + +
460D ILE* 1.3 84.9 - - + +
462D ARG* 1.3 55.9 + - - +
464D PHE* 3.3 5.5 + - + +
465D ALA* 2.9 29.6 + - - +
476D LEU* 3.8 23.8 - - + +
602D TPP 3.3 39.3 - - + +
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Residues in contact with ARG 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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457D THR* 3.2 33.2 + - - +
458D TYR 3.1 8.2 + - - +
459D GLY* 2.9 11.0 + - - +
461D LEU* 1.3 75.4 - - - +
463D TRP* 1.3 61.6 + - - +
465D ALA* 3.4 9.8 + - - +
466D GLY* 3.2 17.0 + - - -
473D VAL 5.5 3.0 + - - -
476D LEU* 4.0 31.6 - - + +
477D ASP* 3.0 32.7 + - - -
525D SER* 5.7 1.8 - - - -
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Residues in contact with TRP 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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282D GLN* 6.3 2.9 - - + -
378D SER* 6.4 0.4 - - - -
459D GLY 3.1 9.7 + - - +
460D ILE* 3.1 17.5 + - + +
462D ARG* 1.3 73.8 - - - +
464D PHE* 1.3 81.1 + + - +
466D GLY* 2.8 22.6 + - - -
467D VAL* 3.0 50.3 + - + +
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Residues in contact with PHE 464 (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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26B SER* 4.1 20.4 - - - -
29B LEU* 3.4 20.9 - - + -
281D TYR* 3.8 42.6 - + - -
282D GLN* 4.7 20.2 - - + -
460D ILE* 3.0 34.7 + - + +
461D LEU* 3.6 4.7 - - - +
463D TRP* 1.3 95.0 - + - +
465D ALA* 1.3 62.6 + - - +
467D VAL* 3.1 15.2 + - + +
468D LEU* 3.0 39.5 + - + +
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Residues in contact with ALA 465 (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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29B LEU* 3.8 10.0 - - + +
461D LEU 2.9 17.2 + - - +
462D ARG* 3.5 11.2 - - - +
463D TRP 3.1 0.2 - - - -
464D PHE* 1.3 76.0 - - - +
466D GLY* 1.3 56.1 + - - +
468D LEU* 4.8 0.2 - - - -
469D GLU* 3.1 3.5 + - - -
470D ALA* 2.9 52.2 + - + +
473D VAL* 4.8 6.7 - - + -
476D LEU* 4.4 14.1 - - + -
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Residues in contact with GLY 466 (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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462D ARG 3.2 8.9 + - - -
463D TRP* 2.8 10.1 + - - -
465D ALA* 1.3 78.3 - - - +
467D VAL* 1.3 57.5 + - - -
468D LEU 3.3 0.4 - - - -
469D GLU* 3.2 23.8 + - - +
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Residues in contact with VAL 467 (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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463D TRP* 3.0 60.9 + - + +
464D PHE* 3.1 12.8 + - + +
466D GLY* 1.3 75.6 - - - +
468D LEU* 1.3 79.8 + - + +
469D GLU* 4.2 7.0 - - - +
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Residues in contact with LEU 468 (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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26B SER 5.1 2.0 - - - +
29B LEU* 4.4 14.6 - - + -
30B PRO* 4.2 30.7 - - + -
33B LYS* 5.9 2.2 - - + +
160B TYR* 5.5 8.7 - - + -
464D PHE* 3.0 26.5 + - + +
465D ALA 4.4 0.2 - - - +
467D VAL* 1.3 95.6 - - + +
469D GLU* 1.3 71.1 + - - +
470D ALA* 3.2 12.9 + - + +
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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