Contacts of the strand formed by residues 486 - 491 (chain A) in PDB entry 4I1R
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 486 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446A LEU* 4.3 22.9 - - + +
449A MET* 3.6 11.0 - - + -
450A GLN* 3.6 46.0 - - + +
457A ASN* 3.3 30.5 - - + +
459A PHE* 4.9 2.5 - - + -
484A ALA* 3.8 18.8 - - + +
485A ASN* 1.3 75.4 - - - +
487A VAL* 1.3 69.5 + - - +
488A PHE* 4.3 6.3 - - + +
551A ARG 3.7 1.3 - - - +
552A SER* 3.5 3.3 - - - -
553A SER* 3.2 33.8 + - - +
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Residues in contact with VAL 487 (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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456A LEU* 3.7 16.6 - - + -
457A ASN 2.9 9.6 + - - +
458A VAL* 3.6 9.0 - - + +
459A PHE 2.9 25.6 + - - -
485A ASN 3.7 2.2 - - - +
486A ILE* 1.3 76.1 - - - +
488A PHE* 1.3 60.7 + - - +
489A GLY 3.7 1.2 + - - -
525A ILE* 3.7 33.2 - - + -
526A THR* 3.9 27.6 - - + -
529A LEU* 3.7 26.5 - - + -
550A ILE* 5.1 2.2 - - + -
551A ARG 3.6 4.7 - - - +
552A SER* 4.4 2.0 - - - +
554A LEU* 4.2 8.3 - - + -
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Residues in contact with PHE 488 (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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423A SER* 5.3 1.8 - - - -
442A VAL* 3.6 22.0 - - + -
443A GLN* 6.0 1.8 - - - -
446A LEU* 4.1 14.8 - - + -
459A PHE* 3.5 30.3 - + + -
461A LEU* 3.6 35.2 - - + -
486A ILE* 3.9 10.7 - - + -
487A VAL* 1.3 72.3 - - - +
489A GLY* 1.3 56.2 + - - +
490A TYR* 3.6 30.3 - + + -
529A LEU* 4.6 1.8 - - - -
549A GLU* 3.5 3.0 - - - +
550A ILE* 3.2 8.1 - - - +
551A ARG* 2.7 83.9 + - + +
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Residues in contact with GLY 489 (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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459A PHE 2.8 15.8 + - - +
460A LEU* 3.4 18.5 - - - +
461A LEU* 2.9 27.9 + - - +
487A VAL 3.7 2.2 + - - -
488A PHE* 1.3 72.7 - - - +
490A TYR* 1.3 59.5 + - - +
491A ALA 4.0 0.9 - - - -
511A PHE* 5.2 1.0 - - - -
529A LEU* 4.0 12.1 - - - +
548A LEU* 4.2 8.7 - - - -
549A GLU 3.6 3.4 - - - -
550A ILE* 4.7 0.2 - - - -
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Residues in contact with TYR 490 (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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417A TYR 5.0 0.7 + - - -
418A GLU* 2.6 38.4 + - - +
423A SER* 3.5 17.6 - - - -
461A LEU* 3.5 27.8 - - + -
463A MET* 3.8 28.5 - - + +
466A LYS* 5.1 0.9 - - - +
488A PHE* 3.6 24.9 - + + -
489A GLY* 1.3 72.6 - - - +
491A ALA* 1.4 59.7 + - - +
492A THR* 4.1 18.9 - - + +
547A ALA 3.0 6.8 - - - +
548A LEU* 3.8 3.7 - - - +
549A GLU* 2.8 60.9 + - + +
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Residues in contact with ALA 491 (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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461A LEU 2.8 15.9 + - - +
462A ASP* 3.8 17.7 - - - +
463A MET* 3.3 23.2 + - - +
489A GLY 4.0 0.2 - - - -
490A TYR* 1.4 74.3 - - - +
492A THR* 1.3 66.9 + - - +
493A CYS* 3.8 7.4 - - - +
511A PHE* 4.0 28.7 - - + -
536A MET* 5.5 0.7 - - + -
547A ALA* 3.4 8.5 - - + -
548A LEU* 4.0 5.3 - - + +
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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