Contacts of the strand formed by residues 740 - 745 (chain A) in PDB entry 5BPW
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 HIS 740 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLU* 3.3 31.5 + - + -
17A LYS 3.6 9.7 + - - -
18A GLN* 4.4 19.4 - - + +
716A SER 4.9 2.8 + - - -
717A MET* 3.4 38.3 + - - -
718A LYS* 3.9 12.8 - - + -
733A VAL 3.8 0.3 - - - +
734A LEU* 3.6 4.4 - - - +
735A SER* 2.3 47.4 + - - +
737A ASN* 3.5 13.4 + - - +
738A LEU 3.6 2.0 - - - -
739A ARG* 1.3 77.9 - - - +
741A VAL* 1.3 67.3 + - - +
742A ARG* 4.6 1.4 + - - -
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Residues in contact with VAL 741 (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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16A GLU* 3.4 11.0 - - - +
17A LYS* 3.1 33.9 + - + +
19A LEU* 3.7 19.1 - - + -
26A LEU* 5.8 0.2 - - + -
37A LEU* 5.1 4.5 - - + -
52A PHE* 3.7 50.5 - - + -
717A MET* 4.8 0.2 - - - -
732A CYS* 4.5 10.1 - - - -
733A VAL 3.3 7.0 - - - +
734A LEU* 3.6 21.5 - - + -
739A ARG 4.2 0.2 + - - -
740A HIS* 1.3 80.1 + - - +
742A ARG* 1.3 60.8 + - - +
743A VAL* 4.9 0.4 - - + -
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Residues in contact with ARG 742 (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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13A VAL* 3.6 25.8 - - + -
15A GLY 3.5 2.5 - - - -
16A GLU* 3.0 35.4 + - - +
712A ARG* 5.6 4.6 - - - +
714A LEU* 4.1 4.6 - - - +
715A GLU* 3.0 49.4 + - - +
716A SER* 4.3 3.2 + - - -
717A MET* 3.4 43.3 - - + +
732A CYS* 3.6 0.3 - - - -
733A VAL 2.9 33.9 + - - -
740A HIS* 4.6 2.2 + - - -
741A VAL* 1.3 75.7 - - - +
743A VAL* 1.3 61.6 + - - +
744A PHE* 3.5 33.7 - - + -
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Residues in contact with VAL 743 (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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13A VAL* 3.6 3.8 - - - +
14A VAL 2.8 24.6 + - - -
15A GLY 2.6 23.2 + - - +
28A TRP* 4.2 10.3 - - + -
49A LEU* 3.5 34.1 - - + +
52A PHE* 3.3 39.3 - - + -
730A VAL* 3.9 4.5 - - + -
731A SER 3.4 11.7 - - - +
732A CYS* 4.1 11.9 - - + -
741A VAL* 4.9 0.4 - - + -
742A ARG* 1.3 77.6 - - - +
744A PHE* 1.3 62.6 + - - +
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Residues in contact with PHE 744 (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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11A PHE* 4.0 15.7 - - + -
12A ARG 3.2 9.6 - - - +
13A VAL* 3.4 32.8 - - + -
14A VAL* 4.3 0.2 - - - -
666A LEU* 4.2 5.8 - - + -
712A ARG* 3.9 16.6 - - - -
714A LEU* 3.8 17.5 - - + -
730A VAL* 3.0 7.4 - - - +
731A SER 2.9 35.8 + - - -
733A VAL* 3.8 23.1 - - + -
742A ARG* 3.5 41.7 - - + -
743A VAL* 1.3 73.7 - - - +
745A GLU* 1.3 65.6 + - - +
746A MET* 3.5 27.4 + - + +
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Residues in contact with GLU 745 (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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12A ARG* 2.8 38.1 + - + +
14A VAL* 3.4 31.8 - - + +
49A LEU* 4.6 5.1 - - + +
728A ARG* 3.5 37.3 + - - +
729A LYS* 5.3 1.1 - - + -
730A VAL* 4.4 5.2 - - - +
744A PHE* 1.3 70.2 - - - +
746A MET* 1.3 61.3 + - - +
747A ASP* 3.4 8.4 - - + +
748A ILE* 3.7 34.4 + - + +
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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