Contacts of the helix formed by residues 394 - 406 (chain D) in PDB entry 5HP1
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 GLN 394 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358C ARG* 4.3 18.9 - - - +
370C GLU* 5.8 5.2 - - + +
373C GLN* 6.1 0.2 - - - +
407C GLN* 3.3 26.2 + - - +
408C ALA 4.6 1.8 + - - +
393D ILE* 1.3 80.3 - - - +
395D LYS* 1.3 68.8 + - - +
396D GLU* 3.4 13.4 + - + +
397D THR* 3.3 18.3 + - - +
398D TRP* 3.0 19.8 + - - +
416D PHE* 4.5 0.4 - - - -
418D ASN* 4.5 7.1 + - - +
22E C 5.0 1.6 + - - -
23E C 3.4 30.3 + - - -
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Residues in contact with LYS 395 (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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393D ILE 3.6 2.0 + - - -
394D GLN* 1.3 77.3 - - - +
396D GLU* 1.3 72.1 + - - +
398D TRP* 3.1 3.1 + - - +
399D GLU* 2.8 67.3 + - - +
416D PHE* 3.5 39.6 - - + +
23E C 4.8 15.9 + - - +
24E G 3.0 33.0 + - - +
2H FRU 3.4 19.8 + - - -
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Residues in contact with GLU 396 (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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356C ARG* 3.8 8.5 + - - -
358C ARG* 2.7 46.6 + - - +
370C GLU* 6.2 1.8 - - + -
373C GLN* 3.9 17.7 - - + +
394D GLN* 3.4 9.4 + - + +
395D LYS* 1.3 92.9 + - - +
397D THR* 1.3 59.3 + - - +
399D GLU* 3.9 7.0 - - - +
400D THR* 2.7 36.0 + - - +
23E C 5.4 0.3 + - - -
24E G 5.7 0.9 + - - -
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Residues in contact with THR 397 (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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369C THR* 4.9 2.3 - - - +
373C GLN* 2.5 32.3 + - - +
408C ALA 4.3 7.4 + - - +
409C THR* 4.4 10.3 + - - +
410C TRP 4.5 3.8 - - - +
365D VAL* 4.1 16.3 - - + +
393D ILE* 4.0 19.3 - - + -
394D GLN* 3.3 20.9 + - - +
395D LYS 3.2 0.6 - - - -
396D GLU* 1.3 80.9 - - - +
398D TRP* 1.3 63.5 + - - +
400D THR 3.5 2.1 + - - -
401D TRP* 3.2 31.5 - - + +
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Residues in contact with TRP 398 (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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365D VAL* 4.3 9.0 - - + -
368D LEU* 3.9 24.2 - - + -
369D THR* 3.2 39.3 - - + -
372D VAL* 4.5 13.9 - - + -
391D LEU* 3.8 12.3 - - + -
393D ILE* 3.6 27.2 - - + +
394D GLN 3.0 10.2 + - - +
395D LYS 3.6 6.1 - - - +
397D THR* 1.3 76.0 - - - +
399D GLU* 1.3 61.9 + - + +
401D TRP 3.2 0.9 + - - -
402D TRP* 2.9 58.4 + + + +
406D TRP* 4.7 5.6 - + - -
414D TRP* 3.3 46.1 - + - -
416D PHE* 3.6 35.7 - + + -
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Residues in contact with GLU 399 (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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395D LYS* 2.8 59.7 + - + +
396D GLU* 4.1 8.0 - - - +
398D TRP* 1.3 77.9 - - + +
400D THR* 1.3 62.0 + - - +
401D TRP 3.5 0.2 + - - -
402D TRP* 3.8 19.6 + - + +
403D THR* 5.4 3.1 + - - +
414D TRP* 5.7 0.4 - - + +
416D PHE* 4.4 4.9 - - + -
2H FRU 2.7 37.7 + - - +
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Residues in contact with THR 400 (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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373C GLN* 4.1 21.4 + - + +
376C THR* 3.9 20.8 - - + +
377C THR* 4.4 11.3 + - - +
380C ILE* 5.6 4.8 - - + +
396D GLU* 2.7 25.0 + - - +
397D THR 3.8 4.5 - - - -
399D GLU* 1.3 79.2 - - - +
401D TRP* 1.3 93.0 + - + +
403D THR* 5.0 4.6 + - - -
404D GLU* 5.4 2.1 - - - +
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Residues in contact with TRP 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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372C VAL* 5.2 1.1 - - + -
373C GLN* 4.4 14.2 - - + +
376C THR* 3.4 33.2 - - + -
380C ILE* 5.8 2.0 - - + -
386C THR* 4.1 12.3 - - + -
410C TRP* 3.8 39.2 + + - -
412C PRO* 3.5 41.5 - - + -
365D VAL* 4.0 17.7 - - + -
397D THR* 3.2 32.2 + - + +
398D TRP 3.2 2.2 + - - -
400D THR* 1.3 100.2 - - + +
402D TRP* 1.3 65.8 + - - +
403D THR* 3.2 3.1 - - - -
404D GLU* 2.9 37.5 + - + +
405D TYR* 3.8 14.4 - - + -
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Residues in contact with TRP 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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24D TRP* 4.4 17.5 - + - -
61D PHE* 3.9 6.7 - + - -
78D ARG* 4.6 4.0 - - - -
365D VAL* 4.8 2.9 - - - +
369D THR* 4.1 10.3 + - - +
398D TRP* 2.9 63.0 + + + +
399D GLU* 3.8 20.2 + - - +
400D THR 3.9 0.2 - - - -
401D TRP* 1.3 76.0 - - - +
403D THR* 1.3 84.7 + - + +
405D TYR* 3.1 16.5 + - - +
406D TRP* 3.2 57.0 + + + +
411D ILE* 3.8 29.4 - - + -
414D TRP* 3.7 26.0 - + - -
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Residues in contact with THR 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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24D TRP* 4.2 18.8 + - + +
30D LYS* 3.6 24.1 + - - -
61D PHE* 3.8 28.1 - - + -
63D ILE* 4.5 1.2 - - - +
399D GLU 5.4 2.8 + - - +
400D THR 5.0 4.0 + - - -
401D TRP 4.6 2.3 + - - -
402D TRP* 1.3 117.5 - - + +
404D GLU* 1.3 64.7 + - - +
405D TYR 3.3 0.3 + - - -
406D TRP* 3.7 12.5 + - - +
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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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27D THR* 4.0 17.2 + - - +
29D GLU* 4.2 13.2 - - - +
30D LYS* 3.3 29.9 - - - +
400D THR 5.4 2.0 - - - +
401D TRP* 2.9 32.8 + - + +
403D THR* 1.3 81.7 + - - +
405D TYR* 1.3 77.0 + - + +
406D TRP 3.7 0.6 - - - +
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Residues in contact with TYR 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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410C TRP* 3.7 17.2 - + - -
363D ASN* 2.4 35.1 + - - -
365D VAL* 4.4 3.4 - - + -
366D LYS* 3.6 53.6 - - + -
369D THR* 3.9 28.6 - - + +
370D GLU* 5.6 2.7 - - + +
373D GLN* 4.0 5.2 + - - -
401D TRP* 3.8 29.1 - - + +
402D TRP 3.1 2.8 + - - +
404D GLU* 1.3 92.8 - - + +
406D TRP* 1.3 65.1 + - - +
407D GLN* 3.4 16.5 + - - +
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Residues in contact with TRP 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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61D PHE* 4.5 1.8 - + + -
63D ILE* 3.1 26.8 - - + +
74D LEU* 3.7 14.6 - - + -
369D THR* 3.5 27.6 - - + -
372D VAL* 4.1 16.2 - - + -
373D GLN* 3.6 28.0 - - + -
398D TRP* 4.7 4.0 - + - -
402D TRP* 3.2 44.5 + + + +
403D THR* 3.7 7.8 + - - +
404D GLU 3.7 1.8 - - - +
405D TYR* 1.3 76.8 - - - +
407D GLN* 1.3 60.6 + - - +
408D ALA* 3.3 22.8 + - + -
410D TRP* 2.9 39.4 + + - -
411D ILE* 4.0 7.1 - - + +
412D PRO* 3.5 29.2 - - + -
414D TRP* 4.5 7.4 - + - -
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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