Contacts of the strand formed by residues 449 - 457 (chain A) in PDB entry 1IVV
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 ARG 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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448A ASN* 1.3 76.0 - - - +
450A VAL* 1.3 65.3 + - - +
451A GLU* 3.8 32.0 + - - +
476A VAL* 4.6 15.8 - - + +
496A ILE 3.6 0.2 - - - +
497A ILE* 3.3 5.9 - - - +
498A SER* 2.7 52.8 + - - +
500A PRO* 3.5 28.5 - - + +
509A PRO* 3.8 27.2 - - - +
577A ILE 3.8 8.7 - - - +
578A ASP* 3.7 15.7 - - - +
579A GLY 3.6 12.8 - - - +
582A ILE* 3.9 1.1 - - - -
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Residues in contact with VAL 450 (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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449A ARG* 1.3 83.0 - - - +
451A GLU* 1.3 71.3 + - - +
476A VAL* 3.4 3.6 - - - +
477A LEU* 2.8 54.2 + - + +
495A TRP* 4.3 15.3 - - + -
496A ILE 3.2 7.4 - - - +
497A ILE* 3.9 20.6 - - + -
541A LEU* 4.6 2.7 - - + -
543A VAL* 4.2 18.2 - - + -
577A ILE* 4.7 1.4 + - + +
582A ILE* 3.6 20.4 - - + +
584A VAL* 4.1 12.1 - - + -
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Residues in contact with GLU 451 (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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449A ARG* 3.8 35.0 + - - +
450A VAL* 1.3 81.5 - - - +
452A GLU* 1.3 61.8 + - - +
453A GLU 3.7 0.9 + - - +
474A ARG* 3.5 49.2 + - + +
475A THR 3.2 5.6 - - - +
476A VAL* 4.0 19.9 + - + +
477A LEU* 5.0 0.4 - - - -
495A TRP* 3.4 4.7 - - - +
496A ILE* 2.8 45.1 + - + +
498A SER* 4.1 7.7 + - - +
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Residues in contact with GLU 452 (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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451A GLU* 1.3 72.5 - - - +
453A GLU* 1.3 59.6 + - - +
454A ASP* 3.9 7.3 + - - +
473A LYS* 3.4 2.6 - - - +
474A ARG* 3.4 2.6 - - - -
475A THR* 2.7 41.8 + - - +
477A LEU* 4.6 9.5 - - + +
485A ARG* 2.8 45.3 + - - +
486A GLU 4.3 0.3 - - - +
493A ARG* 3.4 44.9 + - + +
494A THR 3.7 2.9 - - - -
495A TRP* 2.9 32.4 + - + +
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Residues in contact with GLU 453 (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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451A GLU 3.7 1.8 + - - -
452A GLU* 1.3 70.8 - - - +
454A ASP* 1.3 68.7 + - - +
472A ARG* 2.8 38.8 + - + +
473A LYS 3.2 10.3 - - - +
474A ARG* 2.8 33.3 + - + -
492A GLY 3.8 3.3 - - - +
493A ARG* 3.3 4.5 - - - -
494A THR* 3.0 42.9 + - - +
496A ILE* 3.5 10.3 - - + +
513A LYS* 2.7 29.5 + - - -
593B PHE* 4.3 8.9 - - + -
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Residues in contact with ASP 454 (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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452A GLU* 3.9 8.2 + - - +
453A GLU* 1.3 74.9 - - - +
455A VAL* 1.3 67.3 + - - +
456A VAL* 3.9 0.2 - - - +
472A ARG* 3.2 4.6 - - - +
473A LYS* 2.8 63.4 + - + +
491A THR* 3.7 16.9 + - + +
492A GLY 5.3 0.2 - - - -
493A ARG* 2.9 55.3 + - - +
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Residues in contact with VAL 455 (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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454A ASP* 1.3 77.5 - - - +
456A VAL* 1.3 68.7 + - - +
457A ARG* 4.1 3.1 + - + +
470A PHE* 4.8 0.2 - - + -
471A SER 3.8 9.6 - - - +
472A ARG* 4.3 0.9 - - - +
491A THR* 2.8 40.6 + - - +
492A GLY* 4.4 10.7 - - - +
520B PRO* 4.7 6.1 - - + -
523B LEU* 3.5 39.5 - - + -
591B THR* 4.1 10.5 - - + -
593B PHE* 3.7 26.7 - - + -
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Residues in contact with VAL 456 (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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455A VAL* 1.3 79.8 - - - +
457A ARG* 1.3 73.4 + - - +
458A GLN* 4.1 4.2 - - + +
470A PHE* 3.5 3.5 - - - +
471A SER* 2.7 55.2 + - - +
472A ARG 3.7 2.2 - - - +
473A LYS* 3.6 46.9 - - + +
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Residues in contact with ARG 457 (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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455A VAL* 4.1 2.6 + - + +
456A VAL* 1.3 85.3 - - - +
458A GLN* 1.3 61.5 + - - +
470A PHE* 4.7 4.7 - - - -
522B LEU 4.0 10.2 + - - -
523B LEU* 2.8 47.9 + - + +
524B ALA 2.8 26.7 + - - -
525B ASP* 4.4 0.6 - - - +
526B PRO* 4.0 17.5 - - - +
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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