Contacts of the helix formed by residues 395 - 400 (chain D) in PDB entry 4PKY
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 395 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D GLU* 3.6 22.8 + - - +
371D GLY* 3.5 19.4 - - - +
372D ILE* 3.9 15.3 - - + +
373D PHE* 4.5 0.7 - - - -
393D GLY 4.1 0.6 + - - -
394D LYS* 1.3 74.5 - - - +
396D ILE* 1.3 79.5 + - - +
397D VAL* 3.0 29.4 + - + +
398D GLU* 3.1 38.9 + - + +
399D PHE* 3.5 6.4 - - - -
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Residues in contact with ILE 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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367D HIS* 3.8 20.4 - - + +
371D GLY* 3.0 15.8 + - - +
373D PHE* 3.7 27.3 - - + -
394D LYS 3.9 1.2 + - - -
395D ASN* 1.3 77.5 + - - +
397D VAL* 1.3 65.5 + - + +
399D PHE* 3.1 15.3 + - - +
400D CYS* 3.5 9.1 + - - +
408D LEU* 3.6 29.4 - - + -
412D PHE* 3.8 18.2 - - + -
427D PHE* 4.2 22.2 - - + -
429D PHE* 4.5 11.8 - - + -
441D THR* 5.8 2.0 - - + -
459D CYS* 5.7 1.3 - - - -
461D ASN* 4.6 12.1 - - - +
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Residues in contact with VAL 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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370D GLU 5.7 1.8 - - - +
371D GLY* 6.1 0.2 - - - -
395D ASN* 3.0 21.3 + - - +
396D ILE* 1.3 73.4 - - + +
398D GLU* 1.3 64.2 + - - +
399D PHE 3.0 2.2 - - - -
400D CYS* 3.0 20.9 + - + +
405D GLN* 3.7 37.6 + - + +
408D LEU* 3.9 23.3 - - + -
409D ARG* 4.1 41.3 - - + +
412D PHE* 5.9 0.9 - - + -
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Residues in contact with GLU 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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394D LYS* 3.9 26.5 - - - +
395D ASN* 3.1 37.3 + - + +
397D VAL* 1.3 78.0 - - - +
399D PHE* 1.3 63.2 + - + +
400D CYS 3.4 0.4 - - - -
405D GLN* 5.6 1.2 + - - +
430D ARG* 3.1 31.8 + - - -
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Residues in contact with PHE 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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373D PHE* 4.5 5.6 - + - -
386D TYR* 3.8 28.0 - + - -
390D GLU 4.4 1.8 - - - -
391D LEU* 3.4 28.9 - - + -
394D LYS* 3.5 45.3 - - + -
395D ASN 3.5 12.1 - - - -
396D ILE* 3.1 10.9 + - - +
397D VAL 3.0 0.8 - - - -
398D GLU* 1.3 82.1 - - + +
400D CYS* 1.3 60.1 + - - +
429D PHE* 3.2 40.2 - + + -
430D ARG* 2.8 49.0 + - + +
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Residues in contact with CYS 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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396D ILE 3.5 1.9 + - - +
397D VAL* 3.0 17.9 + - - +
399D PHE* 1.3 79.9 - - - +
401D HIS* 1.3 76.8 - - - +
402D PRO* 3.5 2.9 - - - +
404D ASP* 3.7 28.0 - - - -
405D GLN* 3.4 22.9 + - + -
408D LEU* 3.4 34.3 - - + -
427D PHE* 3.9 9.4 - - + -
428D ARG 3.5 3.8 - - - -
430D ARG* 4.2 8.0 + - - -
436D TRP* 3.9 2.2 - - - -
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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