Contacts of the strand formed by residues 799 - 803 (chain A) in PDB entry 1PD0
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 799 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758A SER 3.7 0.3 - - - -
759A LEU* 2.8 50.8 + - + -
760A HIS* 3.0 23.9 + - + +
798A GLY* 1.3 73.2 - - - -
800A TYR* 1.3 65.4 + - - +
810A LEU* 3.7 30.5 - - + -
811A TRP 3.5 14.1 - - - +
812A MET* 3.8 24.2 - - + -
820A LEU* 4.4 9.2 - - + -
824A VAL* 3.9 27.1 - - + -
848A PHE* 4.1 13.0 - - + -
852A VAL* 4.5 3.6 - - + -
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Residues in contact with TYR 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756A VAL* 4.8 1.8 - - + -
757A TYR 3.2 4.7 - - - +
758A SER* 3.3 25.3 + - - -
759A LEU* 4.6 1.3 - - - +
760A HIS* 3.3 19.1 - + - -
787A ILE* 3.6 27.4 - - + -
793A LEU 2.6 28.7 + - - -
794A PHE* 3.5 43.7 - + + -
795A GLU* 2.8 20.4 + - - +
798A GLY* 3.6 18.4 - - - -
799A LEU* 1.3 75.1 - - - +
801A LEU* 1.3 59.6 + - - +
802A ILE* 4.2 0.7 - - + -
809A PHE 3.5 0.4 - - - +
810A LEU* 3.5 7.5 - - - +
811A TRP* 2.7 57.5 + + + +
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Residues in contact with LEU 801 (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 VAL* 3.4 3.3 - - - -
757A TYR* 2.8 47.0 + - + +
759A LEU* 4.0 22.6 - - + +
800A TYR* 1.3 74.6 - - - +
802A ILE* 1.3 63.1 + - - +
808A LEU* 4.4 10.5 - - + -
809A PHE 3.2 17.0 - - - +
810A LEU* 4.2 11.9 - - + -
855A ILE* 3.6 20.9 - - + -
856A ILE* 4.3 21.3 - - + -
859A LEU* 3.5 30.7 - - + -
871A LEU* 4.4 10.8 - - + -
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Residues in contact with ILE 802 (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 PRO* 4.1 17.9 - - + -
755A ASP 3.7 4.0 - - - +
756A VAL* 4.4 10.3 - - + -
794A PHE* 4.2 30.5 - - + -
800A TYR 5.2 0.7 - - - -
801A LEU* 1.3 78.1 - - - +
803A ASP* 1.3 65.7 + - - +
804A ASN 4.1 1.6 - - - +
807A GLU 3.8 0.7 - - - +
808A LEU* 3.1 9.5 - - - +
809A PHE* 2.8 60.1 + - + +
811A TRP* 5.3 4.0 - - + -
898A ALA* 4.1 12.1 - - + +
901A THR* 3.2 37.2 - - + +
902A LEU* 4.2 5.4 - - + -
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Residues in contact with ASP 803 (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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750A LYS* 3.1 32.1 + - - +
754A PRO* 3.5 2.6 - - - +
755A ASP* 2.9 40.3 + - + +
757A TYR* 4.6 4.7 - - + -
801A LEU 4.1 0.2 + - - -
802A ILE* 1.3 73.7 - - - +
804A ASN* 1.3 57.7 + - - +
805A GLY 3.2 5.4 + - - -
807A GLU 3.7 0.2 - - - -
808A LEU* 3.3 19.7 - - + -
859A LEU* 3.8 28.5 - - + +
869A GLN* 2.5 30.8 - - - +
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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