Contacts of the strand formed by residues 409 - 417 (chain D) in PDB entry 4XH9
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 ILE 409 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378D ASP* 3.7 35.0 - - + +
380D ARG* 3.9 20.9 - - + +
381D ILE* 3.9 20.0 - - + -
384D SER* 4.2 0.2 - - - +
406D PHE* 2.9 46.5 + - + +
408D ASP* 1.3 83.0 - - - +
410D LEU* 1.3 63.0 + - - +
411D VAL* 4.5 0.9 - - + -
430D PRO* 3.6 28.7 - - + -
431D ILE 3.5 16.4 - - - +
432D PRO* 3.8 10.5 - - + -
433D VAL* 3.5 6.2 - - - +
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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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403D ILE* 3.8 24.2 - - + -
404D PHE 3.4 7.6 - - - +
405D LEU* 4.0 19.5 - - + -
409D ILE* 1.3 73.0 - - - +
411D VAL* 1.3 62.7 + - - +
412D LEU* 3.7 25.9 + - + +
430D PRO* 3.4 2.4 - - - +
431D ILE* 2.7 50.3 + - + +
433D VAL* 4.7 0.6 - - - +
436D LEU* 3.9 26.7 - - + -
468D ILE* 3.7 24.2 - - + -
496D ILE* 4.3 17.7 - - + -
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Residues in contact with VAL 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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369D LEU* 4.4 7.2 - - + -
381D ILE* 3.7 32.3 - - + -
402D TYR 3.9 0.7 - - - +
403D ILE* 3.5 2.4 - - - +
404D PHE* 2.8 48.6 + - + +
406D PHE* 3.9 18.8 - - + -
409D ILE* 4.5 1.8 - - + -
410D LEU* 1.3 79.2 - - - +
412D LEU* 1.3 67.9 + - - +
413D THR* 3.8 19.7 - - + -
426D VAL* 4.1 24.0 - - + -
430D PRO* 4.0 9.9 - - + -
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Residues in contact with LEU 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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401D LEU* 4.0 19.5 - - + -
402D TYR 4.1 2.0 - - - -
403D ILE* 4.1 16.6 - - + -
410D LEU* 3.7 24.0 - - + +
411D VAL* 1.3 74.2 - - - +
413D THR* 1.3 56.7 + - - +
426D VAL* 3.5 4.7 - - - +
427D TYR* 2.6 48.5 + - + +
429D GLN 4.5 7.6 - - - +
430D PRO* 5.2 1.8 - - - +
431D ILE* 4.2 13.5 - - + -
468D ILE* 4.1 7.6 - - + -
479D HIS* 3.7 50.7 - - + +
481D LEU* 4.4 3.6 - - + -
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Residues in contact with THR 413 (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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369D LEU* 3.8 18.6 - - + -
401D LEU* 3.4 9.1 - - - +
402D TYR* 2.5 61.4 + - - +
404D PHE* 3.7 24.2 - - + -
411D VAL* 3.8 7.9 - - + -
412D LEU* 1.3 81.6 - - - +
414D ARG* 1.3 61.9 + - - +
424D TYR* 3.6 19.6 - - + +
425D GLN 3.2 9.9 - - - -
426D VAL* 4.2 4.9 - - - -
427D TYR* 3.9 3.4 - - - +
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Residues in contact with ARG 414 (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 HIS* 3.2 47.9 + - + -
400D LYS 5.2 2.7 - - - +
401D LEU* 3.6 19.3 - - + +
413D THR* 1.3 71.0 - - - +
415D PRO* 1.3 67.2 - - + +
416D VAL* 3.8 1.7 - - + +
425D GLN* 2.6 60.3 + - - +
427D TYR* 3.3 45.3 + - + +
428D ARG* 5.2 1.4 - - - +
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Residues in contact with PRO 415 (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 LYS 4.0 15.9 - - - +
402D TYR* 3.5 27.6 - - + +
413D THR* 3.6 8.7 - - - +
414D ARG* 1.3 86.5 - - + +
416D VAL* 1.3 58.1 + - - +
422D HIS* 3.0 29.8 + - + +
423D SER 3.3 7.2 - - - +
424D TYR* 3.8 13.2 - - + -
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Residues in contact with VAL 416 (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* 5.0 7.0 - - - +
414D ARG* 3.8 2.0 - - + +
415D PRO* 1.3 75.9 - - - +
417D THR* 1.3 77.9 + - - +
422D HIS* 2.9 11.6 - - - -
423D SER* 2.6 52.6 + - - +
425D GLN* 3.8 35.9 - - + +
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Residues in contact with THR 417 (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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416D VAL* 1.3 89.2 - - - +
418D ARG* 1.3 64.7 + - - +
421D ARG 3.8 4.0 - - - -
422D HIS* 2.9 34.3 - - + +
423D SER* 5.5 0.9 - - - -
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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