Contacts of the strand formed by residues 812 - 819 (chain A) in PDB entry 3L4U
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 ALA 812 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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751A PRO* 3.9 6.6 - - - +
752A LEU* 2.9 27.8 + - - +
810A ASN* 3.7 4.2 + - - +
811A LEU* 1.3 78.7 - - - +
813A PHE* 1.3 64.8 + - - +
814A ASN* 3.5 3.4 + - + +
857A ASP* 3.2 28.5 - - - +
858A LEU 3.2 20.0 - - - +
859A LEU* 4.0 8.1 - - + -
860A LEU 4.0 1.6 - - - +
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Residues in contact with PHE 813 (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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736A PRO* 4.8 2.5 - - + -
752A LEU* 3.3 27.1 - - + +
753A GLY 3.6 19.7 - - - -
754A LEU* 3.7 26.2 - - + -
768A LEU* 3.8 19.7 - - + -
787A CYS* 5.0 2.0 - - - -
789A PHE* 3.6 30.7 - + - -
798A VAL* 5.0 9.4 - - + -
812A ALA* 1.3 72.1 - - - +
814A ASN* 1.3 58.8 + - - +
815A GLU 3.6 6.3 - - - +
816A ILE* 5.3 3.4 - - + -
856A ILE* 3.5 9.6 - - - +
857A ASP* 3.5 0.5 - - - -
858A LEU* 2.8 60.4 + - + +
859A LEU 5.3 0.7 - - - -
860A LEU* 4.1 22.7 - - + -
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Residues in contact with ASN 814 (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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751A PRO* 3.4 33.9 - - + +
752A LEU 2.9 19.1 + - - +
753A GLY* 5.0 0.2 - - - -
812A ALA* 3.5 3.0 + - + +
813A PHE* 1.3 73.1 - - - +
815A GLU* 1.3 67.6 + - - +
854A THR* 3.8 13.3 - - - +
855A ASP 4.2 3.2 + - - +
856A ILE* 3.2 29.1 - - - +
857A ASP* 5.4 3.1 - - - +
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Residues in contact with GLU 815 (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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752A LEU 3.8 0.6 + - - -
753A GLY* 3.3 8.5 - - - -
754A LEU 3.1 21.5 + - - -
813A PHE* 3.6 2.2 - - - +
814A ASN* 1.3 92.0 + - - +
816A ILE* 1.3 71.1 + - - +
817A LYS* 4.3 10.3 - - - +
852A ILE* 3.5 34.4 - - + +
853A ILE 3.2 7.2 - - - +
854A THR* 3.9 11.1 - - + +
856A ILE* 3.9 1.2 - - - +
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Residues in contact with ILE 816 (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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754A LEU* 3.5 17.9 - - + +
756A ILE* 3.5 33.2 - - + -
796A LEU* 3.8 24.2 - - + -
813A PHE* 5.3 3.4 - - + -
815A GLU* 1.3 83.7 - - - +
817A LYS* 1.3 59.7 + - - +
818A ILE* 4.1 10.9 + - + -
851A ALA 3.8 0.9 - - - +
852A ILE* 3.4 1.4 - - - -
853A ILE* 2.7 55.3 + - + +
856A ILE* 4.2 22.7 - - + -
858A LEU* 4.2 19.3 - - + -
866A VAL* 4.8 3.6 - - + -
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Residues in contact with LYS 817 (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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703A TYR* 3.9 21.8 + - - -
704A GLU 4.6 7.9 + - - -
705A THR 5.2 2.0 - - - -
706A GLY* 4.7 7.1 - - - +
754A LEU 2.9 11.6 + - - +
755A ILE* 3.4 23.1 - - + +
756A ILE* 2.8 33.3 + - - +
815A GLU* 4.3 10.5 - - - +
816A ILE* 1.3 74.1 - - - +
818A ILE* 1.3 55.4 + - - +
819A LEU* 3.8 29.5 + - + +
850A VAL* 4.1 11.7 - - + -
851A ALA 3.4 3.6 - - - -
852A ILE* 3.9 26.2 - - + -
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Residues in contact with ILE 818 (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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756A ILE* 3.5 17.3 - - + +
758A LEU* 3.9 19.5 - - + -
816A ILE* 4.1 15.9 - - + +
817A LYS* 1.3 76.2 - - - +
819A LEU* 1.3 63.6 + - - +
821A THR* 3.7 28.5 - - + +
824A PRO* 4.9 6.1 - - + -
850A VAL* 3.4 7.1 - - - +
851A ALA* 2.8 45.1 + - + +
853A ILE* 3.9 26.2 - - + -
868A TRP* 4.3 30.7 - - + -
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Residues in contact with LEU 819 (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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701A TYR* 3.7 44.0 - - + -
702A ASP 5.2 1.3 - - - +
703A TYR 6.1 0.4 - - - +
706A GLY* 3.8 11.4 - - - +
729A LEU* 4.0 13.0 - - + -
755A ILE* 3.8 24.9 - - + -
756A ILE 2.8 16.2 + - - +
757A ALA* 4.2 4.3 - - + -
758A LEU* 3.1 30.1 + - - +
817A LYS* 3.8 33.7 - - + +
818A ILE* 1.3 72.1 - - - +
820A GLY* 1.3 64.4 + - - +
821A THR 3.4 2.0 - - - -
849A LYS 4.1 1.6 - - - -
850A VAL* 3.8 19.7 - - + -
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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