Contacts of the strand formed by residues 423 - 430 (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 LEU 423 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411D SER* 3.8 17.3 - - - +
414D GLN* 3.6 37.0 - - + -
415D VAL* 3.7 26.0 - - + -
418D LEU* 3.6 21.3 - - + -
421D GLN 4.1 0.2 + - - -
422D VAL* 1.3 87.2 - - - +
424D SER* 1.3 62.0 + - - +
425D VAL* 4.3 1.6 - - + -
441D THR 3.8 0.2 - - - +
442D SER* 3.1 4.5 - - - -
443D SER* 2.8 32.9 + - - +
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Residues in contact with SER 424 (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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422D VAL* 5.6 1.3 - - - -
423D LEU* 1.3 78.3 - - - +
425D VAL* 1.3 62.2 + - - +
440D ARG* 4.4 17.8 - - - +
441D THR 3.4 6.6 + - - -
442D SER* 4.2 9.6 - - - +
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Residues in contact with VAL 425 (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 LEU* 3.7 33.9 - - + +
408D LEU* 5.1 7.6 - - + -
411D SER* 3.7 24.7 - - - +
423D LEU* 6.1 1.1 - - + -
424D SER* 1.3 75.5 - - - +
426D MET* 1.3 72.7 + - - +
427D PHE* 4.2 13.7 - - + -
439D MET 3.9 0.2 - - - +
440D ARG* 3.5 6.6 - - - +
441D THR* 2.7 63.4 + - + +
443D SER* 5.5 1.6 - - - +
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Residues in contact with MET 426 (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 ASP* 5.0 0.9 - - - -
407D LEU* 3.3 23.0 - - + +
425D VAL* 1.3 77.2 - - - +
427D PHE* 1.3 68.0 + - - +
438D TRP* 3.7 24.5 - - + -
439D MET 3.4 9.6 - - - +
440D ARG* 4.6 16.6 - - + -
464D VAL* 4.5 20.2 - - - -
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Residues in contact with PHE 427 (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* 4.2 17.3 - - + -
400D CYS* 3.9 7.6 - - + -
404D ASP* 3.9 18.4 - - + +
407D LEU* 5.2 0.7 - - + -
408D LEU* 3.6 30.1 - - + -
425D VAL* 4.2 17.7 - - + -
426D MET* 1.3 81.2 - - - +
428D ARG* 1.3 69.4 + - - +
429D PHE* 3.9 27.4 - + + -
437D LEU 3.5 0.5 - - - +
438D TRP* 3.5 13.3 - - - -
439D MET* 2.6 61.2 + - + +
441D THR* 3.1 30.7 - - + -
461D ASN* 4.8 2.0 - - - -
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Residues in contact with ARG 428 (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 CYS* 3.5 1.6 - - - -
401D HIS* 3.1 60.2 + - + -
403D GLU* 2.9 43.0 + - - +
404D ASP* 2.9 30.9 + - - +
427D PHE* 1.3 85.2 - - - +
429D PHE* 1.3 59.8 + - - +
436D TRP* 4.1 19.7 - - + -
437D LEU 3.3 5.8 - - - +
438D TRP* 3.5 48.4 - - + +
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Residues in contact with PHE 429 (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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363D PHE* 5.7 5.6 - + - -
373D PHE* 4.9 6.5 - + - -
384D VAL* 3.4 41.7 - - + -
386D TYR* 4.0 5.2 - + - -
391D LEU* 4.5 13.9 - - + -
396D ILE* 4.5 15.3 - - + -
399D PHE* 3.2 42.0 - + + -
427D PHE* 3.9 20.9 - + + -
428D ARG* 1.3 74.0 - - - +
430D ARG* 1.3 89.1 + - - +
431D SER* 3.3 3.2 + - - -
435D GLU 3.3 0.3 - - - +
436D TRP* 3.7 3.1 - - - -
437D LEU* 2.7 36.6 + - + +
439D MET* 3.5 25.1 - - + -
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Residues in contact with ARG 430 (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 TYR* 3.3 23.0 - - - +
398D GLU 3.1 26.0 + - - -
399D PHE* 2.8 30.0 + - + +
400D CYS 4.2 7.9 + - - -
402D PRO* 5.2 6.1 - - - +
405D GLN* 5.4 3.0 - - - +
429D PHE* 1.3 82.8 - - - +
431D SER* 1.3 61.1 + - - +
434D GLN* 5.7 2.7 - - - -
435D GLU 3.6 7.4 - - - +
436D TRP* 3.4 37.8 - - + -
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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