Contacts of the helix formed by residues 400 - 412 (chain D) in PDB entry 5YD6
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 THR 400 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399D ASP* 1.3 76.8 + - - +
401D GLN* 1.3 58.4 + - - +
403D ILE* 3.3 3.8 + - - +
404D GLN* 2.9 31.2 + - + +
581D LEU 5.8 0.7 - - - +
582D VAL* 3.8 35.7 - - + +
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Residues in contact with GLN 401 (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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514C GLU* 4.2 25.1 + - - +
521C PRO* 6.1 3.2 - - - +
525C GLU* 5.0 12.4 + - - +
399D ASP* 2.8 28.4 + - - +
400D THR* 1.3 78.9 - - + +
402D HIS* 1.3 59.6 + - + +
404D GLN* 3.4 6.7 + - - +
405D GLN* 3.0 44.6 + - - +
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Residues in contact with HIS 402 (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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399D ASP* 3.6 31.8 + - - +
400D THR 3.4 0.6 - - - -
401D GLN* 1.3 76.5 - - + +
403D ILE* 1.3 59.7 + - - +
405D GLN* 3.5 17.2 + - - +
406D PHE* 3.0 20.3 + - - +
474D GLN* 3.8 23.6 + - - -
477D ARG* 4.0 31.8 - - + -
478D GLY* 3.4 27.4 - - - +
479D PHE* 5.9 0.2 - - - -
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Residues in contact with ILE 403 (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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399D ASP 3.4 21.9 + - - +
400D THR 3.3 6.8 + - - +
402D HIS* 1.3 74.3 - - - +
404D GLN* 1.3 63.7 + - - +
406D PHE* 3.4 8.2 + - - +
407D TYR* 3.1 52.6 + - + +
477D ARG 4.3 5.8 - - - +
478D GLY* 4.3 0.9 - - - +
572D ARG* 3.9 20.6 - - - +
576D LEU* 3.8 26.0 - - + -
579D GLU* 4.8 7.4 - - - +
582D VAL* 3.8 27.1 - - + -
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Residues in contact with GLN 404 (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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400D THR* 2.9 19.7 + - + +
401D GLN* 3.7 7.6 - - - +
403D ILE* 1.3 74.5 - - - +
405D GLN* 1.3 59.8 + - - +
407D TYR* 3.2 23.1 + - - +
408D ASP* 2.9 61.3 + - - +
582D VAL* 4.2 12.3 - - + +
583D PRO 4.9 2.9 - - - +
585D PRO* 5.2 6.9 - - - +
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Residues in contact with GLN 405 (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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525C GLU* 3.7 24.0 + - - -
386D ARG* 3.3 37.4 - - - +
401D GLN* 3.0 33.9 + - - +
402D HIS* 3.5 23.5 + - + +
403D ILE 3.4 0.2 - - - -
404D GLN* 1.3 74.6 - - - +
406D PHE* 1.3 57.7 + - - +
408D ASP* 3.9 10.7 + - - +
409D LEU* 3.1 39.6 + - + +
470D LEU* 6.1 2.7 - - + -
479D PHE* 5.7 0.2 - - - -
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Residues in contact with PHE 406 (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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402D HIS 3.0 16.9 + - - +
403D ILE 3.4 7.6 - - - +
404D GLN 3.2 0.2 - - - -
405D GLN* 1.3 74.2 - - - +
407D TYR* 1.3 77.1 + + - +
409D LEU* 3.6 2.8 + - - +
410D LEU* 3.4 45.8 + - + +
478D GLY 3.5 20.2 - - - +
479D PHE* 3.4 56.1 - + + +
482D TRP* 3.8 21.3 - + - -
569D GLY 5.2 0.2 - - - -
572D ARG* 4.3 11.0 - - + -
573D ILE* 4.3 17.0 - - + -
576D LEU* 4.1 21.3 - - + -
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Residues in contact with TYR 407 (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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403D ILE* 3.1 31.9 + - + +
404D GLN* 3.5 24.7 - - - +
406D PHE* 1.3 84.3 - + - +
408D ASP* 1.3 59.0 + - - +
410D LEU* 3.0 6.2 + - + +
411D THR* 2.8 31.9 + - - +
573D ILE* 5.4 4.9 - - + -
576D LEU* 3.3 35.5 - - + +
582D VAL* 3.0 28.4 + - + -
583D PRO 3.6 10.8 - - - -
584D PRO* 3.6 22.6 - - + +
585D PRO* 3.6 25.1 - - + -
588D ILE* 3.7 21.5 - - + -
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Residues in contact with ASP 408 (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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522C LYS* 5.9 3.3 + - - +
404D GLN* 2.9 49.5 + - - +
405D GLN* 3.9 10.3 - - + +
407D TYR* 1.3 74.5 - - - +
409D LEU* 1.3 55.9 + - + +
411D THR* 3.4 9.2 + - - +
412D GLY* 2.8 33.1 + - - -
585D PRO* 6.1 0.2 - - - +
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Residues in contact with LEU 409 (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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386D ARG* 4.8 9.6 - - - +
405D GLN* 3.1 25.5 + - + +
406D PHE 3.9 4.0 - - - +
407D TYR 3.3 0.2 - - - -
408D ASP* 1.3 75.9 - - + +
410D LEU* 1.3 55.3 + - - +
412D GLY* 4.3 0.7 - - - -
413D SER* 2.7 30.8 + - - -
447D PHE* 3.3 9.1 - - + -
464D PHE* 3.6 64.3 - - + -
466D ASN* 4.5 12.6 - - - +
468D VAL* 4.7 9.9 - - + -
470D LEU* 4.1 13.5 - - + -
479D PHE* 4.0 14.4 - - + -
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Residues in contact with LEU 410 (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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406D PHE* 3.4 49.5 + - + +
407D TYR 3.0 7.3 + - - +
409D LEU* 1.3 76.1 - - - +
411D THR* 1.3 63.4 + - - +
413D SER* 3.3 9.2 + - - -
414D MET* 3.4 4.1 - - - +
443D PHE* 3.3 28.8 - - + -
444D LEU* 3.6 26.5 - - + -
447D PHE* 3.7 34.5 - - + -
482D TRP* 5.1 1.1 - - + -
573D ILE* 4.5 5.4 - - + -
588D ILE* 4.1 21.8 - - + -
601D 8SU 4.4 8.7 - - + -
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Residues in contact with THR 411 (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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407D TYR 2.8 22.0 + - - +
408D ASP* 3.4 14.6 + - - -
410D LEU* 1.3 71.7 - - - +
412D GLY* 1.3 59.2 + - - +
413D SER 3.1 0.4 - - - -
414D MET* 3.0 29.7 + - - +
415D GLU* 4.3 3.3 + - - +
585D PRO* 3.8 13.5 - - + -
587D ILE* 3.7 28.7 - - + -
588D ILE* 3.8 18.2 - - + -
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Residues in contact with GLY 412 (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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408D ASP 2.8 22.8 + - - -
409D LEU* 4.3 1.6 - - - -
411D THR* 1.3 71.7 + - - +
413D SER* 1.3 57.8 + - - +
414D MET 3.4 0.4 + - - -
415D GLU* 5.0 1.0 + - - +
416D ILE* 3.9 13.3 + - - +
465D CYS* 3.9 11.7 - - - -
466D ASN* 5.8 2.3 - - - +
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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