Contacts of the strand formed by residues 749 - 755 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683A ARG* 5.9 5.2 - - - -
710A GLU* 3.9 22.4 - - + -
711A ILE 3.2 31.0 - - - +
712A PRO* 3.4 26.9 - - + -
713A GLU* 3.7 5.9 + - - -
745A SER* 3.3 3.5 + - - -
746A GLU 2.8 38.0 + - - +
747A ASN* 3.7 26.9 - - - -
748A GLY* 1.4 76.6 - - - +
750A ILE* 1.3 68.9 + - - +
751A LYS* 3.8 11.6 + - + +
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Residues in contact with ILE 750 (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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709A LYS 3.4 3.6 - - - +
710A GLU* 3.5 1.4 - - - -
711A ILE* 2.8 53.7 + - + +
712A PRO 5.0 0.2 - - - +
713A GLU* 3.7 34.5 - - + +
719A SER* 6.3 3.6 - - - +
722A LEU* 5.6 8.5 - - + -
726A ILE* 3.8 29.2 - - + -
743A SER* 5.0 3.6 - - - -
744A PHE 3.9 9.9 - - - +
745A SER* 4.6 6.7 - - - -
749A PHE* 1.3 72.4 - - - +
751A LYS* 1.3 64.9 + - - +
752A ILE* 4.1 7.6 + - + -
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Residues in contact with LYS 751 (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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673A TYR* 2.7 31.9 + - + +
675A TYR* 3.0 21.9 + - - +
708A ILE* 4.0 7.0 - - + -
709A LYS 3.3 4.3 - - - -
710A GLU* 3.8 23.3 - - + +
743A SER* 3.1 26.9 - - - -
744A PHE* 2.9 19.2 + - + +
746A GLU* 3.0 21.4 + - + +
747A ASN* 2.8 36.5 + - - +
749A PHE* 4.3 9.4 - - + +
750A ILE* 1.3 73.7 - - - +
752A ILE* 1.4 60.8 + - - +
753A PHE* 3.8 14.5 - - + -
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Residues in contact with ILE 752 (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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707A ALA 3.6 1.0 - - - +
708A ILE* 3.3 4.6 - - - -
709A LYS* 2.7 58.0 + - + +
711A ILE* 3.5 30.7 - - + -
726A ILE* 4.2 30.7 - - + -
729A HIS* 4.8 4.9 - - - +
740A TYR* 3.7 29.6 - - + -
742A GLY 3.8 2.7 - - - -
743A SER* 4.1 3.4 - - - -
750A ILE* 4.6 2.9 - - + -
751A LYS* 1.4 74.7 - - - +
753A PHE* 1.3 65.2 + - - +
754A MET* 4.0 16.6 + - + +
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Residues in contact with PHE 753 (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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671A LEU* 3.6 24.7 - - + -
673A TYR* 3.6 27.4 - + - -
706A ILE* 3.8 7.4 - - + -
707A ALA 3.5 2.7 - - - +
708A ILE* 3.6 31.4 - - + -
740A TYR* 3.6 1.7 - - - -
741A LEU* 2.7 43.4 + - + -
742A GLY* 2.8 28.7 + - - +
743A SER* 4.1 0.4 - - - -
744A PHE* 3.4 44.2 - + - -
751A LYS* 3.8 26.2 - - + -
752A ILE* 1.3 73.3 - - - +
754A MET* 1.3 60.9 + - - +
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Residues in contact with MET 754 (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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1A IE4 3.9 31.2 - - + -
694A VAL* 4.6 4.3 - - + -
706A ILE* 3.6 5.6 - - - +
707A ALA* 2.7 38.5 + - + +
709A LYS* 3.7 39.7 - - + +
729A HIS* 4.3 12.3 - - + -
738A VAL* 3.9 21.8 - - + -
739A GLN 3.2 14.4 - - - +
740A TYR* 4.3 5.4 - - - -
741A LEU* 3.6 8.3 - - - -
752A ILE* 4.0 15.5 - - + +
753A PHE* 1.3 79.4 - - - +
755A GLU* 1.3 64.9 + - - +
756A GLN 3.5 0.2 + - - -
822A ASP 6.0 0.9 - - - -
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Residues in contact with GLU 755 (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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1A IE4 2.9 23.6 + - - -
705A ARG 5.1 2.7 - - - -
738A VAL* 3.6 5.3 - - + -
739A GLN* 2.7 52.3 + - + +
741A LEU* 3.8 12.8 - - + +
754A MET* 1.3 74.6 - - - +
756A GLN* 1.3 62.4 + - - +
757A VAL* 4.5 9.8 - - + +
819A LYS* 2.8 42.0 + - - +
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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