Contacts of the strand formed by residues 749 - 755 (chain B) in PDB entry 4BIC
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 PHE 749 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683B ARG* 5.7 4.5 - - - -
710B GLU* 4.1 27.6 - - + -
711B ILE 3.5 5.2 - - - +
712B PRO* 3.6 41.5 - - + -
713B GLU* 3.5 4.4 + - - +
745B SER* 3.3 4.3 - - - -
746B GLU 2.9 29.4 + - - +
747B ASN* 3.4 38.6 - - - -
748B GLY* 1.4 79.5 - - - +
750B ILE* 1.3 68.1 + - - +
751B LYS* 3.7 12.9 + - + +
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Residues in contact with ILE 750 (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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709B LYS 3.3 3.2 - - - +
710B GLU* 3.4 3.5 - - - -
711B ILE* 2.7 51.9 + - + +
712B PRO 4.7 2.2 - - - +
713B GLU* 3.8 32.5 - - + +
719B SER* 5.9 2.7 - - - +
722B LEU* 5.4 11.0 - - + -
726B ILE* 4.2 24.5 - - + -
743B SER* 5.2 2.7 - - - -
744B PHE 3.6 9.6 - - - +
745B SER* 3.9 10.1 - - - +
749B PHE* 1.3 72.2 - - - +
751B LYS* 1.3 64.5 + - - +
752B ILE* 4.4 9.9 - - + -
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Residues in contact with LYS 751 (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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673B TYR* 2.9 31.2 + - + +
675B TYR* 3.0 23.0 + - - +
708B ILE* 3.9 8.5 - - + -
709B LYS 3.3 3.4 - - - -
710B GLU* 3.8 23.1 - - + -
743B SER* 3.0 26.0 - - - -
744B PHE* 2.7 23.0 + - + +
746B GLU* 3.1 26.4 + - + +
747B ASN* 2.7 34.0 + - - +
749B PHE* 4.0 7.6 - - + +
750B ILE* 1.3 77.2 - - - +
752B ILE* 1.4 60.0 + - - +
753B PHE* 3.7 16.7 - - + -
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Residues in contact with ILE 752 (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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707B ALA 3.5 4.2 - - - +
708B ILE* 3.5 1.8 - - - -
709B LYS* 2.9 46.4 + - + +
711B ILE* 3.5 32.3 - - + -
726B ILE* 4.0 27.1 - - + -
729B HIS* 5.2 4.9 - - + -
740B TYR* 4.0 22.9 - - + -
742B GLY 3.6 2.7 - - - -
743B SER* 3.9 13.5 - - - -
750B ILE* 4.4 5.4 - - + -
751B LYS* 1.4 73.9 - - - +
753B PHE* 1.3 62.3 + - - +
754B MET* 3.9 24.0 + - + +
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Residues in contact with PHE 753 (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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671B LEU* 3.7 23.3 - - + -
673B TYR* 3.7 16.2 - + - -
706B ILE* 3.3 26.5 - - + -
707B ALA 3.5 1.8 - - - +
708B ILE* 3.7 21.8 - - + -
740B TYR* 3.6 1.0 - - - -
741B LEU* 2.6 44.5 + - + -
742B GLY* 2.7 29.2 + - - +
743B SER* 4.2 0.9 - - - -
744B PHE* 3.4 46.4 - + - -
751B LYS* 3.7 27.4 - - + -
752B ILE* 1.3 74.6 - - - +
754B MET* 1.3 58.3 + - - +
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Residues in contact with MET 754 (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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2A IE4 3.7 40.8 - - + -
694B VAL* 4.5 4.0 - - + -
706B ILE* 3.5 7.3 - - - +
707B ALA 2.7 36.3 + - - +
709B LYS* 3.8 33.0 - - + +
729B HIS* 4.3 14.8 - - - +
738B VAL* 4.2 9.4 - - + -
739B GLN 3.1 16.6 - - - +
740B TYR* 4.3 5.8 - - - -
741B LEU* 3.6 8.5 - - - -
752B ILE* 4.0 23.1 - - + +
753B PHE* 1.3 78.5 - - - +
755B GLU* 1.3 62.3 + - - +
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Residues in contact with GLU 755 (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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2A IE4 2.9 22.7 + - - -
705B ARG 5.0 2.2 - - - -
706B ILE* 4.9 1.6 - - - +
707B ALA* 3.7 0.2 - - - +
738B VAL* 3.6 6.8 - - + -
739B GLN* 2.7 48.0 + - + +
741B LEU* 3.8 12.9 - - + +
754B MET* 1.3 76.4 - - - +
756B GLN* 1.3 63.3 + - - +
757B VAL* 4.7 6.4 - - + +
819B LYS* 3.2 43.9 + - - +
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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