Contacts of the strand formed by residues 790 - 794 (chain A) in PDB entry 5AMN
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 LEU 790 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717A TRP* 3.6 26.3 - - + -
776A PHE* 3.5 35.0 - - + -
779A LEU* 3.9 32.6 + - + +
780A LYS* 3.6 27.6 - - + +
782A VAL 5.7 1.2 + - - -
788A ILE* 3.9 3.2 + - - +
789A LYS* 1.3 83.1 - - - +
791A TYR* 1.3 61.1 + - - +
792A GLY 3.7 16.8 - - - +
802A LEU* 4.6 5.6 - - + -
803A ILE 3.6 17.5 - - - +
804A VAL* 4.3 12.1 - - + +
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Residues in contact with TYR 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A LYS 4.9 2.6 - - - +
717A TRP* 3.5 17.9 - - - -
746A LEU* 3.4 44.4 - - + +
747A LYS* 5.3 11.5 - - + +
749A ARG* 4.3 29.3 + - - -
753A THR* 4.8 3.7 - - + +
754A THR 5.2 0.4 - - - -
755A VAL* 3.7 17.3 - - + -
789A LYS* 4.5 12.2 - - + +
790A LEU* 1.3 79.3 - - - +
792A GLY* 1.3 57.1 + - - +
803A ILE* 2.7 19.8 + - + +
804A VAL 3.7 15.9 - - - -
805A GLU* 3.6 32.2 + - + +
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Residues in contact with GLY 792 (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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717A TRP* 3.1 23.8 - - - -
719A PHE* 5.1 3.6 - - - -
746A LEU* 5.9 0.4 - - - -
776A PHE* 4.5 1.6 - - - -
790A LEU* 3.7 11.0 - - - +
791A TYR* 1.3 81.8 - - - +
793A ALA* 1.3 63.0 + - - +
802A LEU 3.9 0.2 - - - -
803A ILE* 2.9 33.3 + - - +
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Residues in contact with ALA 793 (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 PHE* 5.4 0.9 - - + -
717A TRP 2.7 11.7 + - - +
718A GLU* 3.5 11.0 - - - +
719A PHE 2.9 23.6 + - - +
776A PHE* 3.8 30.3 - - + -
792A GLY* 1.3 75.6 - - - +
794A CYS* 1.3 65.0 + - - +
795A SER* 4.1 1.8 - - - +
800A LEU* 4.5 10.1 - - + -
801A LEU 3.1 15.0 - - - +
802A LEU* 4.4 5.6 - - + -
803A ILE* 4.2 4.1 - - - +
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Residues in contact with CYS 794 (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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718A GLU* 4.0 4.0 - - - -
719A PHE* 3.2 26.0 - - - +
721A ARG* 3.6 39.5 - - + +
724A LEU* 4.1 25.4 - - - -
793A ALA* 1.3 75.0 - - - +
795A SER* 1.3 61.4 + - - +
796A GLN 5.4 0.4 - - - +
799A PRO 3.4 1.7 - - - +
800A LEU* 3.1 8.5 - - - +
801A LEU* 2.9 36.9 + - + -
803A ILE* 4.1 8.5 - - - -
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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