Contacts of the strand formed by residues 477 - 482 (chain B) 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 LYS 477 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B THR 3.5 2.6 - - - +
470B LEU* 4.9 1.8 - - - -
471B GLU* 3.0 51.7 + - + +
474B PRO* 6.3 0.7 - - + -
475B ARG* 3.7 4.2 + - + +
476B PHE* 1.3 79.0 - - - +
478B VAL* 1.3 66.4 + - - +
479B SER* 4.1 24.8 + - - +
493B ASP* 5.3 13.0 + - - -
70C ASP* 4.8 12.5 + - - +
75C GLN* 6.3 0.6 - - - +
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Residues in contact with VAL 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B TYR* 3.7 32.3 - - + -
430B GLY 4.0 5.8 - - - +
431B PHE 3.6 27.1 + - - +
432B GLY* 4.0 6.1 - - - -
433B PRO* 4.7 2.0 - - + -
454B LEU* 3.9 16.2 - - + -
468B ASN* 3.6 29.8 - - + +
469B THR 3.1 11.9 - - - +
470B LEU* 4.4 12.3 - - + +
476B PHE* 4.5 5.6 - - + -
477B LYS* 1.3 77.6 - - - +
479B SER* 1.3 66.7 + - - +
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Residues in contact with SER 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B PRO* 4.3 2.7 - - - -
468B ASN* 3.4 5.8 - - - -
469B THR* 2.9 46.5 + - - -
471B GLU* 4.5 6.9 + - - -
477B LYS* 4.1 28.5 + - - +
478B VAL* 1.3 79.3 - - - +
480B PRO* 1.4 76.6 - - - +
67C TYR* 5.1 2.8 + - - -
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Residues in contact with PRO 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B GLY* 5.9 0.2 - - - -
433B PRO* 3.7 14.3 - - + -
468B ASN* 3.7 11.0 - - - +
469B THR* 4.3 2.4 + - - -
479B SER* 1.4 96.9 - - - +
481B TYR* 1.3 63.3 + - - +
484B THR* 4.6 9.4 - - - +
493B ASP* 5.7 3.8 - - - +
495B HIS* 3.3 52.7 - - + +
67C TYR* 5.8 1.2 - - - -
83C TYR* 4.8 9.4 - - - -
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Residues in contact with TYR 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B TRP* 3.7 33.0 - + + -
467B ILE* 3.2 17.7 + - + +
468B ASN* 4.4 0.4 + - - -
469B THR* 4.5 9.2 - - + -
480B PRO* 1.3 75.5 - - - +
482B LEU* 1.3 93.3 + - + +
522B LEU* 4.2 17.4 - - + +
545B PRO* 6.1 0.7 - - + +
64C THR* 3.8 17.1 - - + +
65C CYS 3.0 31.1 + - - -
66C PRO* 4.0 5.2 - - - +
67C TYR* 4.1 22.2 + + + -
83C TYR* 3.7 35.2 + + + +
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Residues in contact with LEU 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B VAL* 4.1 0.3 - - - -
467B ILE* 3.2 40.0 + - + +
480B PRO* 5.2 0.4 - - - +
481B TYR* 1.3 105.7 - - + +
483B PHE* 1.3 101.6 + - + +
484B THR* 2.9 21.6 + - - +
522B LEU* 5.0 3.8 - - + -
524B TYR* 4.4 11.4 - - + +
545B PRO* 5.5 0.9 - - + -
35C PHE* 4.7 9.0 - - + -
61C TYR* 5.4 5.4 - - + -
62C ARG* 5.4 2.7 - - - +
64C THR* 4.2 25.6 - - + +
84C GLU* 6.5 0.4 - - + -
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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