Contacts of the strand formed by residues 834 - 842 (chain A) in PDB entry 4AGD
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 834 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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829A PHE* 3.9 13.0 - - + -
830A PRO 4.1 3.1 - - - +
831A ARG* 3.4 22.7 - - - +
832A ASP* 3.4 3.2 - - - -
833A ARG* 1.3 79.7 - - - +
835A LYS* 1.3 64.2 + - - +
836A LEU* 3.2 49.4 - - + +
851A ALA* 3.9 17.7 - - + -
852A ASP 3.6 0.4 - - - +
853A ALA* 3.4 26.9 - - + -
865A VAL* 4.2 4.9 - - + -
867A VAL* 4.6 4.0 - - + -
905A CYS* 5.1 3.4 - - - -
913A MET* 4.6 11.9 - - - -
915A ILE* 4.6 19.3 - - + -
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Residues in contact with LYS 835 (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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834A LEU* 1.3 73.3 - - - +
836A LEU* 1.3 68.8 + - - +
851A ALA* 3.4 3.1 - - - -
852A ASP* 2.7 67.0 + - + +
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Residues in contact with LEU 836 (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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831A ARG 5.8 0.4 - - - +
834A LEU* 3.2 31.2 - - + +
835A LYS* 1.3 81.8 - - - +
837A GLY* 1.3 58.9 + - - +
849A ILE* 4.2 16.2 - - + -
850A GLU 4.2 0.7 - - - -
851A ALA* 4.2 0.7 - - + -
852A ASP* 5.4 0.8 - - - +
867A VAL* 3.4 37.2 - - + -
869A MET* 4.6 11.9 - - + -
913A MET* 4.8 13.5 - - + -
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Residues in contact with GLY 837 (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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836A LEU* 1.3 77.6 - - - +
838A LYS* 1.3 61.5 + - - -
839A PRO* 3.8 3.6 - - - +
849A ILE* 3.0 15.4 - - - +
850A GLU* 2.9 15.8 + - - -
851A ALA* 5.4 0.2 - - - -
852A ASP* 5.9 1.3 - - - -
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Residues in contact with LYS 838 (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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837A GLY* 1.3 72.3 - - - -
839A PRO* 1.3 77.5 - - + +
840A LEU* 4.6 10.1 - - + -
849A ILE* 3.7 0.4 - - - -
850A GLU* 2.9 58.4 + - + +
2000A B49 4.3 24.0 - - - +
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Residues in contact with PRO 839 (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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837A GLY 3.8 4.0 - - - +
838A LYS* 1.3 95.3 - - + +
840A LEU* 1.3 63.4 + - - +
841A GLY 4.8 2.5 - - - +
842A ARG* 3.6 47.8 - - + +
847A GLN* 4.7 3.6 - - - +
848A VAL 3.7 6.7 - - - +
849A ILE* 4.1 13.9 - - + -
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Residues in contact with LEU 840 (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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838A LYS* 4.6 10.5 - - + +
839A PRO* 1.3 77.1 - - - +
841A GLY* 1.3 60.2 + - - +
848A VAL* 2.7 22.4 + - + +
849A ILE 3.9 4.7 - - - -
850A GLU* 3.5 43.3 - - + +
866A ALA* 4.4 2.0 - - + -
918A PHE* 3.9 22.9 - - + -
2000A B49 3.4 76.8 - - + +
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Residues in contact with GLY 841 (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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839A PRO* 5.0 1.1 - - - +
840A LEU* 1.3 82.7 - - - +
842A ARG* 1.3 63.0 + - - -
847A GLN* 3.2 5.9 - - - +
848A VAL* 2.9 31.8 + - - +
1047A PHE* 4.9 7.0 - - - -
1050A ALA* 3.8 9.9 - - - +
2000A B49 4.3 6.9 - - - +
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Residues in contact with ARG 842 (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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839A PRO* 3.6 31.7 - - + +
841A GLY* 1.3 73.7 - - - -
843A GLY* 1.3 63.7 + - - +
846A GLY 3.8 2.5 - - - -
847A GLN* 4.0 24.8 + - + +
871A LYS* 4.4 17.9 - - + +
1050A ALA 3.2 10.2 - - - +
1052A ASP 4.4 3.3 + - - -
1055A LYS* 4.7 12.8 + - - -
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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