Contacts of the strand formed by residues 438 - 446 (chain C) 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 GLU 438 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436C GLY 4.1 1.2 + - - -
437C ALA* 1.3 71.4 - - - +
439C THR* 1.3 59.5 + - - +
440C PHE* 3.6 22.9 - - + -
459C THR* 2.9 24.1 + - - +
460C ASN* 3.5 17.3 - - - +
461C LYS* 3.4 28.5 + - + +
463C ARG* 2.7 47.6 + - - +
488C ASP 5.3 0.3 - - - +
489C SER* 5.5 2.0 - - - -
492C GLU 4.3 4.3 + - - +
493C VAL* 3.6 7.8 - - + +
494C ASN 3.1 24.7 + - - +
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Residues in contact with THR 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437C ALA 3.4 2.6 + - - -
438C GLU* 1.3 70.9 - - - +
440C PHE* 1.3 63.0 + - - +
441C TYR* 3.5 29.6 + - + +
459C THR* 3.1 25.0 - - - -
460C ASN* 2.8 16.7 + - - -
494C ASN* 3.4 20.0 + - + +
496C VAL* 4.1 9.2 - - + -
287D LYS 4.1 7.6 - - - +
288D ALA* 3.7 4.7 - - - +
289D LEU* 3.3 41.6 + - + -
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Residues in contact with PHE 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438C GLU* 3.6 42.2 - - + -
439C THR* 1.3 74.1 - - - +
441C TYR* 1.3 63.5 + - - +
442C VAL* 3.6 4.6 + - + +
457C TYR* 3.7 29.8 - + + -
458C VAL 3.7 3.4 - - - -
459C THR* 3.6 16.6 - - + -
463C ARG* 4.3 2.9 - - - -
485C ALA* 3.7 37.7 - - + -
488C ASP* 3.8 13.9 - - + -
489C SER* 3.7 26.0 - - - -
493C VAL* 3.4 15.3 - - + -
494C ASN 2.7 12.9 + - - +
495C ILE* 3.4 2.6 - - + -
496C VAL 2.9 25.9 + - - -
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Residues in contact with TYR 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439C THR* 3.5 21.3 - - + +
440C PHE* 1.3 72.1 - - - +
442C VAL* 1.3 61.0 + - - +
457C TYR* 3.1 2.5 - - - -
458C VAL* 2.7 39.4 + - + +
460C ASN 5.0 0.2 - - - -
496C VAL* 3.7 27.1 - - + +
543C GLY* 4.3 3.8 - - - -
544C GLY* 3.6 38.8 - - - +
545C ASN* 3.7 11.4 - - + +
548C VAL* 3.7 5.6 - - - +
254D VAL* 4.3 3.6 - - - +
258D GLN* 3.6 28.4 + - - -
286D THR* 3.6 31.0 - - + -
287D LYS* 2.3 38.8 + - - -
289D LEU* 4.1 2.9 - - - +
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Residues in contact with VAL 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C PHE* 3.9 3.4 - - + +
441C TYR* 1.3 77.6 - - - +
443C ASP* 1.3 66.2 + - - +
456C GLY 3.5 5.4 - - - +
457C TYR* 3.9 7.6 - - + -
478C GLU 5.2 0.7 - - - +
481C ALA* 3.6 22.0 - - + +
482C ILE* 3.8 25.6 - - + -
485C ALA* 3.6 31.4 - - + -
495C ILE* 3.9 12.6 - - + -
496C VAL 3.1 18.1 + - - +
497C THR* 3.9 17.3 + - - +
498C ASP* 4.4 1.6 + - - +
545C ASN* 4.4 5.9 - - - +
548C VAL* 3.9 4.5 - - - +
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Residues in contact with ASP 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C VAL* 1.3 75.8 - - - +
444C GLY* 1.3 67.4 + - - +
455C ALA* 3.6 0.2 - - - -
456C GLY 2.9 32.6 + - - +
478C GLU* 4.8 1.0 - - - +
481C ALA* 3.2 9.5 - - - +
497C THR* 6.1 0.2 - - - -
498C ASP* 3.4 9.9 - - - +
548C VAL* 3.6 25.6 - - + +
549C ASP* 3.0 16.3 - - - +
552C VAL* 3.6 11.4 - - + +
602C MG 2.2 25.8 - - - -
606C MG 2.0 31.9 - - - -
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Residues in contact with GLY 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443C ASP* 1.3 88.2 + - - +
445C ALA* 1.3 62.0 + - - +
454C LYS 3.2 12.3 - - - -
455C ALA* 4.1 0.7 - - - -
474C ASN* 5.0 0.9 - - - +
477C THR* 3.2 28.2 + - - -
478C GLU* 4.1 11.4 - - - +
481C ALA* 4.2 0.6 - - - +
552C VAL* 3.9 4.5 - - - -
606C MG 3.8 5.9 - - - -
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Residues in contact with ALA 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443C ASP* 5.6 0.4 - - - +
444C GLY* 1.3 75.3 - - - +
446C ALA* 1.3 61.8 + - - +
453C GLY* 3.1 2.1 - - - -
454C LYS 2.7 37.7 + - - +
474C ASN* 3.8 7.0 - - - +
477C THR* 3.3 7.9 + - - +
549C ASP* 5.7 0.4 - - - +
552C VAL* 3.5 25.4 - - + +
553C SER 3.8 18.4 - - - +
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Residues in contact with ALA 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445C ALA* 1.3 75.0 - - - +
447C ASN* 1.3 65.1 + - - +
448C ARG* 3.7 2.9 + - - -
452C LEU 3.5 6.5 - - - +
453C GLY* 3.8 0.2 - - - -
472C THR* 3.8 20.0 - - + +
473C THR* 3.4 37.0 - - - -
474C ASN* 2.8 20.7 + - - +
477C THR* 4.1 0.2 + - - -
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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