Contacts of the strand formed by residues 466 - 471 (chain A) in PDB entry 3INB
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 466 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A TYR* 4.8 2.0 - - - +
433A PRO* 4.6 7.0 - - + +
435A ILE* 6.1 0.9 - - + -
437A HIS* 5.2 2.9 - - + -
454A LEU 5.0 0.4 - - - +
455A THR* 3.4 2.9 - - - -
456A ILE* 2.9 55.8 + - + +
464A LEU 4.4 2.9 - - - +
465A GLY* 1.3 75.6 - - - -
467A ILE* 1.3 65.5 + - - +
468A ASN* 3.0 41.5 - - - +
482A LEU 4.1 4.5 - - - -
483A PHE* 4.5 1.8 - - - +
484A THR* 4.0 12.8 - - + +
497A PRO* 4.3 31.6 - - + -
514A LEU* 4.2 0.5 - - - +
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Residues in contact with ILE 467 (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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453A TRP* 3.8 21.8 - - + -
454A LEU 3.9 2.0 - - - -
455A THR* 4.3 15.3 - - + +
465A GLY 4.2 0.4 + - - -
466A VAL* 1.3 81.3 - - - +
468A ASN* 1.3 71.5 + - - +
481A TYR* 3.2 28.0 + - + +
482A LEU* 3.2 29.4 + - + -
483A PHE* 4.0 23.1 - - + -
514A LEU* 3.9 15.5 - - + -
516A ILE* 4.5 7.4 - - + -
522A LEU* 5.1 2.9 - - + -
524A TYR* 4.0 31.4 - - + -
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Residues in contact with ASN 468 (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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410A TYR* 3.0 41.8 + - - -
433A PRO* 3.2 25.0 - - - +
453A TRP* 3.4 16.9 - - - -
454A LEU* 2.8 35.1 + - + +
466A VAL* 3.0 25.8 - - - +
467A ILE* 1.3 79.2 - - - +
469A THR* 1.3 64.4 + - - +
478A VAL* 3.6 12.0 - - + +
479A SER 3.4 9.4 - - - +
480A PRO* 3.8 5.2 - - - +
481A TYR* 4.7 0.7 - - - -
484A THR* 4.3 1.2 + - - -
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Residues in contact with THR 469 (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 VAL* 4.5 12.3 - - + -
452A TYR 3.2 5.8 - - - +
453A TRP* 3.5 27.6 - - + -
454A LEU* 4.9 0.9 - - - -
468A ASN* 1.3 83.2 - - - +
470A LEU* 1.3 61.3 + - - +
471A GLU* 5.7 1.1 - - - -
477A LYS 3.5 2.3 - - - +
478A VAL* 3.1 11.3 - - - +
479A SER* 2.9 47.8 + - - -
480A PRO 4.3 2.6 + - - -
481A TYR* 4.6 4.5 - - + -
67D TYR* 3.9 34.0 - - + -
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Residues in contact with LEU 470 (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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364A LYS* 5.6 0.4 - - + -
412A VAL* 4.0 24.7 - - + -
443A LEU* 4.2 15.5 - - + -
450A ASN 4.0 0.5 - - - +
451A VAL* 3.1 9.0 - - - +
452A TYR* 2.5 56.4 + - + +
454A LEU* 4.6 15.2 - - + +
469A THR* 1.3 73.3 - - - +
471A GLU* 1.3 64.7 + - - +
472A TRP* 3.8 29.2 - - + -
476A PHE* 3.4 35.7 - - + -
477A LYS 4.0 0.4 - - - +
478A VAL* 4.4 11.9 - - + -
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Residues in contact with GLU 471 (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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450A ASN 3.9 5.8 - - - +
451A VAL* 3.4 23.1 - - + +
469A THR* 5.5 2.0 + - - -
470A LEU* 1.3 74.1 - - - +
472A TRP* 1.3 65.8 + - - +
473A ILE 5.0 2.0 - - - +
474A PRO* 5.0 9.9 - - + +
475A ARG 3.8 3.4 - - - +
476A PHE* 3.4 6.1 - - - -
477A LYS* 2.9 55.0 + - + +
479A SER* 4.5 4.5 + - - -
67D TYR* 2.7 30.8 + - + +
69D ARG* 3.7 23.4 - - - +
70D ASP* 4.2 13.8 + - - +
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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