Contacts of the strand formed by residues 378 - 384 (chain A) in PDB entry 4HXG
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 ALA 378 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A PRO* 4.2 2.9 - - + -
372A ILE* 4.1 21.5 - - + +
377A LYS* 1.3 75.6 - - - +
379A PRO* 1.3 74.1 - - + +
380A VAL* 3.8 0.2 - - - +
407A GLY 3.6 14.4 - - - +
409A TYR* 3.6 17.0 - - + -
454A GLN 2.9 7.3 + - - -
455A ALA* 3.6 6.1 - - - -
456A ASP* 3.0 24.4 + - - -
459A ARG* 4.2 0.2 - - - -
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Residues in contact with PRO 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A LYS 4.4 0.2 - - - +
378A ALA* 1.3 93.8 - - + +
380A VAL* 1.3 59.5 + - - +
407A GLY 3.5 13.5 - - - +
408A TYR* 3.7 31.4 - - + -
409A TYR* 2.9 25.3 + - - +
456A ASP* 4.8 0.9 - - + -
459A ARG* 3.5 48.4 - - + +
604A LEU* 4.5 4.0 - - + -
605A LYS* 4.4 16.6 - - - -
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Residues in contact with VAL 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A ALA 3.8 3.1 - - - +
379A PRO* 1.3 82.1 - - - +
381A ILE* 1.3 61.7 + - - +
382A VAL* 4.7 0.2 - - + -
409A TYR* 3.5 14.6 - - + +
411A VAL* 3.9 20.2 - - + -
445A ILE* 6.1 0.7 - - + -
448A PHE* 3.9 19.7 - - + -
449A LEU* 4.9 1.6 - - + -
455A ALA* 3.7 30.3 - - + -
456A ASP 4.3 4.0 - - - +
459A ARG 2.9 13.3 + - - +
460A ILE* 3.3 22.2 - - + -
461A GLY* 2.7 33.3 + - - +
604A LEU* 3.7 2.5 - - - +
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Residues in contact with ILE 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A VAL* 1.3 75.3 - - - +
382A VAL* 1.3 64.4 + - - +
383A PHE* 3.3 28.4 + - + -
403A MET* 3.6 34.5 - - + -
408A TYR* 3.5 31.9 - - + -
409A TYR 2.8 12.2 + - - +
410A ILE* 3.6 4.3 - - + -
411A VAL 3.0 23.4 + - - +
461A GLY 3.5 3.4 - - - +
463A THR* 3.8 17.0 - - + -
600A PHE* 3.6 28.7 - - + -
604A LEU* 4.0 9.0 - - + -
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Residues in contact with VAL 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A VAL* 4.7 0.9 - - + -
381A ILE* 1.3 74.1 - - - +
383A PHE* 1.3 71.9 + - - +
384A VAL* 4.3 4.9 - - + -
411A VAL* 3.2 29.2 - - + +
412A TYR* 5.2 1.3 - - - -
441A ILE* 4.2 24.7 - - + -
445A ILE* 3.6 24.9 - - + -
460A ILE* 4.2 14.4 - - + -
461A GLY 2.7 20.0 + - - +
462A ILE* 3.3 9.4 - - + +
463A THR* 2.8 30.5 + - - +
482A PHE* 4.4 1.8 - - + -
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Residues in contact with PHE 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A ILE* 3.3 33.4 - - + -
382A VAL* 1.3 75.0 - - - +
384A VAL* 1.3 63.8 + - - +
392A TYR* 3.4 25.9 - - + +
397A LYS* 4.1 12.8 - - - -
399A GLU* 3.9 30.5 - - + -
400A MET* 3.6 28.5 - - + -
403A MET* 4.9 1.3 - - + -
410A ILE* 4.0 28.3 - - + -
411A VAL 2.9 7.7 + - - +
412A TYR* 3.4 16.4 - - + +
413A VAL 4.5 1.9 + - - +
441A ILE* 5.9 0.3 - - - +
463A THR* 3.5 22.9 - - + -
464A GLY* 6.1 0.9 - - - -
596A PHE* 4.0 16.8 - + - -
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A VAL* 4.3 5.8 - - + -
383A PHE* 1.3 78.7 - - - +
385A HIS* 1.3 74.4 + - + +
386A GLY 3.9 0.3 + - - -
392A TYR* 3.6 5.8 + - - -
413A VAL 6.0 0.7 - - - -
415A PRO* 5.7 4.3 - - + -
441A ILE* 3.9 29.4 - - + -
462A ILE* 3.9 30.7 - - + -
463A THR 3.0 8.8 + - - +
464A GLY* 3.6 8.8 - - - -
465A ILE 4.2 1.7 + - - -
467A TYR* 4.9 4.0 - - + +
468A GLY* 3.3 22.5 - - - +
471A MET* 3.8 25.4 - - + -
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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