Contacts of the strand formed by residues 441 - 446 (chain A) in PDB entry 5IVK
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 VAL 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A THR* 3.1 27.6 - - + +
345A MET* 4.5 8.1 - - + -
429A LEU* 4.2 23.1 - - + -
432A ARG* 3.6 27.8 - - - +
433A PHE* 4.1 21.1 - - + -
439A THR 3.8 0.2 + - - -
440A PRO* 1.3 75.4 - - - +
442A TYR* 1.3 74.3 + - - +
443A LEU* 4.3 5.4 - - + -
528A PRO* 3.5 3.0 - - - +
529A ILE* 3.1 35.8 + - + +
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Residues in contact with TYR 442 (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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343A THR 2.9 15.3 + - - +
344A MET* 3.3 11.1 - - + +
345A MET 2.9 26.2 + - - +
440A PRO* 3.7 29.9 - - + +
441A VAL* 1.3 76.6 - - - +
443A LEU* 1.3 64.5 + - - +
507A PHE* 4.2 10.5 - + - -
511A GLY 3.4 20.5 + - - -
512A ASN* 3.6 32.8 + - - +
513A PRO* 4.7 5.4 - - + -
526A TRP* 3.5 49.6 - + + +
527A ASP 4.1 2.5 - - - -
528A PRO* 3.6 26.8 - - + +
529A ILE* 5.0 0.2 - - - -
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Residues in contact with LEU 443 (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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345A MET* 3.3 11.0 - - + +
346A GLY* 5.8 0.2 - - - -
422A TRP* 6.1 0.4 - - + -
425A MET* 4.7 15.7 - - + -
429A LEU* 4.2 19.5 - - + -
441A VAL* 4.3 10.5 - - + -
442A TYR* 1.3 80.2 - - - +
444A TYR* 1.3 62.4 + - - +
526A TRP* 3.3 16.0 + - - +
527A ASP 5.7 0.4 + - - -
529A ILE* 3.6 25.6 - - + +
536A TYR* 3.4 41.3 - - + -
537A LYS 3.6 10.9 + - - +
538A CYS* 3.4 6.8 - - + -
539A LEU 3.0 19.8 + - - -
550A VAL* 4.4 8.5 - - + -
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Residues in contact with TYR 444 (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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241A ILE* 4.6 3.1 - - + -
243A MET* 3.2 39.6 - - + +
244A SER* 5.3 0.3 + - - -
344A MET* 3.8 15.5 - - + -
345A MET* 3.0 16.0 + - - +
346A GLY* 3.0 52.0 + - - -
347A ASN* 3.5 9.4 + - - -
422A TRP* 5.0 3.8 - - - -
443A LEU* 1.3 75.0 - - - +
445A ARG* 1.3 62.9 + - - +
446A PHE* 3.9 20.2 - - + -
474A GLU* 4.7 5.9 + - + -
500A MET* 5.2 2.0 - - + -
504A TRP* 3.5 32.6 - + + -
526A TRP* 4.3 12.6 - - + -
538A CYS* 4.3 4.0 - - - +
539A LEU 3.4 11.2 - - - +
541A ILE* 4.1 17.5 - - + -
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Residues in contact with ARG 445 (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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347A ASN 3.3 9.2 - - - +
349A SER* 3.6 38.2 + - - +
422A TRP* 4.3 14.1 - - + -
444A TYR* 1.3 76.7 - - - +
446A PHE* 1.3 60.7 + - - +
447A ASP* 3.5 7.4 + - - -
538A CYS* 3.8 17.7 - - - -
539A LEU 2.9 7.9 + - - +
540A ASN* 2.9 31.4 + - - +
541A ILE* 2.9 26.6 + - - +
548A ILE* 4.5 1.2 - - - +
550A VAL* 5.2 0.2 - - - -
551A PRO* 3.5 33.3 - - - +
552A GLU* 2.9 39.9 + - - -
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Residues in contact with PHE 446 (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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347A ASN 2.8 15.9 + - - +
348A THR* 3.2 11.3 - - + -
349A SER* 2.9 24.9 + - - -
444A TYR* 3.9 14.2 - - + -
445A ARG* 1.3 71.0 - - - +
447A ASP* 1.3 57.2 + - - +
448A PHE* 3.5 39.7 - - + -
469A VAL* 3.8 15.5 - - + +
473A ASP 4.4 2.9 - - - -
474A GLU* 3.8 31.4 - - + +
477A TYR* 3.8 22.7 - + - -
496A THR* 4.1 4.7 - - + -
500A MET* 3.5 44.6 - - + -
541A ILE* 4.0 10.8 - - + -
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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