Contacts of the strand formed by residues 825 - 831 (chain A) in PDB entry 5C58
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 825 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820A LYS* 3.2 6.8 - - - +
821A LEU* 3.1 49.4 + - + -
822A THR* 3.0 25.5 + - + +
824A SER* 1.3 78.3 - - - +
826A THR* 1.3 62.0 + - - +
861A VAL* 4.4 15.9 - - + -
862A GLU 3.5 4.9 - - - +
863A TYR* 3.6 36.6 - - + -
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Residues in contact with THR 826 (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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779A LYS* 5.0 1.2 + - - -
818A SER* 4.6 7.1 - - - -
819A TYR 3.4 11.0 + - - -
820A LYS* 3.6 27.4 - - + +
821A LEU* 5.3 0.2 - - - +
824A SER 4.6 3.6 - - - +
825A LEU* 1.3 78.2 - - - +
827A LEU* 1.3 66.1 + - - +
828A ARG* 3.9 17.4 + - - +
860A GLY 4.3 0.2 - - - +
861A VAL* 5.1 1.7 - - - +
862A GLU* 2.8 66.2 + - + +
864A ARG* 5.8 0.9 - - + +
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Residues in contact with LEU 827 (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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818A SER* 3.4 2.1 - - - -
819A TYR* 3.1 39.2 + - + +
821A LEU* 3.6 42.8 - - + -
826A THR* 1.3 75.3 - - - +
828A ARG* 1.3 61.3 + - - +
860A GLY 3.2 14.1 - - - +
861A VAL* 4.2 17.7 - - + -
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Residues in contact with ARG 828 (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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132A ASP* 3.3 57.0 + - - +
133A ASN* 4.9 4.4 + - - +
135A PRO* 5.7 3.4 - - + -
248A HIS* 4.4 17.4 + - - +
817A ALA 3.1 16.4 - - - +
818A SER* 3.7 15.0 - - - -
826A THR* 3.9 19.0 + - - +
827A LEU* 1.3 75.3 - - - +
829A GLY* 1.3 60.4 + - - +
859A GLY* 3.2 2.9 - - - -
860A GLY* 3.0 35.1 + - - +
862A GLU* 2.8 40.0 + - - +
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Residues in contact with GLY 829 (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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816A TYR* 3.4 1.4 - - - +
817A ALA* 3.1 31.7 + - - +
828A ARG* 1.3 75.0 - - - +
830A SER* 1.3 64.8 + - - -
858A GLN 3.5 12.1 - - - -
859A GLY* 3.9 3.1 - - - -
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Residues in contact with SER 830 (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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133A ASN 4.4 1.1 - - - -
134A ARG* 5.4 0.7 - - - -
135A PRO* 3.5 31.0 - - - +
815A LEU 3.2 15.0 - - - -
816A TYR* 4.2 7.6 - - - +
829A GLY* 1.3 76.3 - - - -
831A VAL* 1.3 68.1 + - - +
856A THR 3.5 0.6 - - - +
857A VAL* 3.3 5.6 - - - +
858A GLN* 2.7 54.6 + - - +
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Residues in contact with VAL 831 (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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134A ARG* 6.1 0.2 - - - +
814A ASP* 3.2 8.3 - - - +
815A LEU* 2.9 51.6 + - + +
830A SER* 1.3 81.7 - - - +
832A GLU* 1.3 61.8 + - - +
833A ASN 3.4 10.8 - - - +
834A LEU* 3.8 22.7 - - + +
855A ARG* 4.0 21.5 - - + -
856A THR 3.2 8.3 - - - +
857A VAL* 3.9 19.1 - - + -
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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