Contacts of the helix formed by residues 400 - 412 (chain D) in PDB entry 3HYW
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 400 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391C TRP* 3.8 15.9 - - + +
388D TYR* 3.5 13.7 - - + +
391D TRP* 4.9 4.3 - - + -
392D LYS* 3.6 8.1 - - + -
397D ASN* 3.6 26.9 - - + +
398D ILE 3.5 7.2 - - - -
399D ALA* 1.4 89.3 - - - +
401D SER* 1.3 65.6 + - - +
402D PHE* 3.2 27.6 - - + -
403D GLU* 3.0 35.7 + - - +
404D GLU* 3.7 3.5 + - - +
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Residues in contact with SER 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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391C TRP* 3.4 12.3 - - - +
394C ARG* 4.4 4.0 + - - -
432C SO4 2.6 31.9 + - - -
397D ASN* 5.0 0.4 - - - +
399D ALA 3.5 3.5 + - - -
400D PRO* 1.3 71.6 - - - +
402D PHE* 1.3 64.0 + - - +
403D GLU 3.3 0.3 + - - -
404D GLU* 3.4 9.0 + - - +
405D LYS* 3.4 39.2 + - - +
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Residues in contact with PHE 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C LYS* 3.9 10.1 - - + +
388C TYR* 3.6 49.8 - + + +
391C TRP* 3.5 43.3 - + + -
402C PHE* 4.6 1.1 - + - -
500C DCQ 4.4 0.7 - - + -
388D TYR* 3.6 27.1 - + - -
391D TRP* 5.8 0.2 - + - -
400D PRO* 3.2 23.8 + - + -
401D SER* 1.3 82.1 + - - +
403D GLU* 1.3 59.2 + - - +
405D LYS* 3.3 11.1 + - - +
406D VAL* 2.9 34.8 + - + +
500D DCQ 3.6 37.5 - - + -
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Residues in contact with GLU 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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318D GLU* 3.9 3.5 - - - +
388D TYR* 2.5 38.5 + - - +
392D LYS* 2.8 27.8 + - - -
398D ILE 4.6 2.0 - - - -
399D ALA* 5.3 2.0 - - - -
400D PRO* 3.0 19.6 + - + +
402D PHE* 1.3 85.2 - - + +
404D GLU* 1.3 65.6 + - - +
406D VAL* 3.3 5.0 + - - +
407D LEU* 3.0 33.9 + - + +
500D DCQ 3.5 42.8 - - + +
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Residues in contact with GLU 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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322D MET* 5.7 3.1 - - - +
400D PRO 3.7 3.5 + - - +
401D SER* 3.4 10.6 + - - +
402D PHE 3.4 0.4 - - - -
403D GLU* 1.3 78.1 - - - +
405D LYS* 1.3 58.9 + - + +
407D LEU* 3.5 8.2 + - + +
408D GLU* 3.0 34.4 + - - +
413D VAL 4.4 2.9 - - - +
414D HIS* 5.0 3.3 - - - +
415D PRO* 3.7 39.2 - - + +
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Residues in contact with LYS 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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387C LYS* 3.7 48.7 - - + +
394C ARG* 5.5 6.4 - - - +
401D SER* 3.6 30.7 + - - +
402D PHE* 3.3 9.3 + - - +
403D GLU 3.3 0.4 - - - -
404D GLU* 1.3 78.3 - - + +
406D VAL* 1.3 57.4 + - - +
408D GLU* 3.3 14.0 + - - +
409D ILE* 2.8 36.1 + - + +
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Residues in contact with VAL 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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384C ALA* 3.8 28.9 - - + +
387C LYS* 5.2 2.0 - - + -
402D PHE* 2.9 23.0 + - + +
403D GLU* 3.8 4.7 - - - +
405D LYS* 1.3 73.2 - - - +
407D LEU* 1.3 65.4 + - + +
409D ILE* 3.3 7.2 + - + -
410D PHE* 2.9 37.4 + - + +
500D DCQ 3.9 35.0 - - + -
600D LMT 3.8 30.1 - - + -
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Residues in contact with LEU 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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315D MET* 4.1 22.0 - - + -
346D ILE* 4.3 13.0 - - + -
403D GLU* 3.0 33.6 + - + +
404D GLU* 3.8 8.3 - - + +
406D VAL* 1.3 80.4 - - + +
408D GLU* 1.3 57.5 + - - +
410D PHE* 5.1 0.9 - - - -
411D LEU* 2.9 34.6 + - + +
412D LYS 3.2 5.0 + - - -
413D VAL* 3.3 26.6 + - + +
500D DCQ 3.8 39.9 - - + -
600D LMT 5.3 4.7 - - + -
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Residues in contact with GLU 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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404D GLU* 3.0 23.5 + - - +
405D LYS* 3.4 13.7 - - - +
407D LEU* 1.3 74.9 - - - +
409D ILE* 1.3 67.1 + - - +
412D LYS* 3.1 25.5 + - - +
413D VAL 3.6 21.5 + - - +
414D HIS* 6.1 1.3 - - + -
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Residues in contact with ILE 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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380C TYR* 3.7 45.1 - - + +
383C THR* 3.9 28.0 - - + -
384C ALA* 4.1 18.6 - - - -
387C LYS* 4.4 12.6 - - + -
405D LYS* 2.8 30.4 + - + +
406D VAL* 3.5 6.7 - - - +
408D GLU* 1.3 77.2 - - + +
410D PHE* 1.3 73.9 + - + +
412D LYS* 4.8 2.8 + - - +
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Residues in contact with PHE 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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377C TRP* 4.5 11.9 - - + -
380C TYR* 3.8 18.6 - + + -
381C PHE* 3.7 29.6 - + + -
384C ALA* 3.7 25.1 - - + -
371D ILE* 5.7 0.7 - - - +
406D VAL* 2.9 29.3 + - + +
407D LEU* 4.8 0.4 - - - +
409D ILE* 1.3 81.8 - - + +
411D LEU* 1.3 66.9 + - + +
412D LYS* 3.8 2.9 + - - +
600D LMT 3.7 66.2 - - + +
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Residues in contact with LEU 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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346D ILE* 3.2 39.7 - - + -
357D PHE* 4.7 2.2 - - + -
359D PHE* 3.8 31.2 - - + -
361D ASP* 4.9 0.9 - - - +
369D ARG* 4.5 7.0 + - - -
371D ILE* 3.6 31.4 - - + -
407D LEU* 2.9 19.4 + - + +
410D PHE* 1.3 81.2 - - + +
412D LYS* 1.3 73.3 - - - +
413D VAL* 3.2 11.1 + - + +
600D LMT 3.8 35.9 - - + -
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Residues in contact with LYS 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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361D ASP* 4.4 5.0 - - - +
369D ARG* 3.6 37.8 + - - +
408D GLU* 3.1 24.4 + - - +
409D ILE 5.4 2.7 - - - +
410D PHE 3.8 1.7 + - - +
411D LEU* 1.3 79.0 - - - +
413D VAL* 1.3 61.4 + - - +
414D HIS* 3.8 10.6 + - - -
431D SO4 3.6 26.5 + - - -
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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