Contacts of the strand formed by residues 923 - 929 (chain B) in PDB entry 5J67
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 GLU 923 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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867B ILE* 3.6 1.9 - - - +
868B HIS* 2.7 54.1 + - + +
908B LEU* 4.4 4.0 - - - -
921B GLY 3.9 9.9 - - - +
922B VAL* 1.3 79.9 - - - +
924B ILE* 1.3 63.5 + - - +
925B ARG* 2.6 37.8 + - - +
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Residues in contact with ILE 924 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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865B CYS* 4.5 1.3 - - + -
866B ILE 3.5 6.5 - - - +
867B ILE* 4.2 14.6 - - + -
901B ILE* 3.8 49.8 - - + +
904B LEU* 4.4 9.2 - - + -
905B SER* 4.1 22.9 - - - +
908B LEU* 4.4 17.5 - - + +
922B VAL* 4.9 1.1 - - + -
923B GLU* 1.3 78.8 - - - +
925B ARG* 1.3 77.9 + - - +
926B CYS* 4.0 16.6 - - - -
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Residues in contact with ARG 925 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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864B THR 4.2 0.7 - - - +
865B CYS* 3.5 1.4 - - - -
866B ILE* 2.9 38.4 + - + +
868B HIS* 4.0 23.5 - - + +
923B GLU* 2.6 40.3 + - - -
924B ILE* 1.3 84.3 + - - +
926B CYS* 1.3 62.9 + - - +
927B GLU* 5.8 0.2 - - - -
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Residues in contact with CYS 926 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863B LEU* 4.0 11.2 - - + -
864B THR 3.5 4.0 - - - -
865B CYS* 2.1 46.2 - - - -
901B ILE* 4.8 0.7 - - - -
924B ILE* 4.0 14.4 - - - -
925B ARG* 1.3 75.0 - - - +
927B GLU* 1.3 67.6 + - - +
941B ARG* 4.3 23.2 + - - +
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Residues in contact with GLU 927 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862B GLU* 4.1 0.9 - - - +
863B LEU* 4.0 2.2 - - - -
864B THR* 2.8 40.9 + - - +
925B ARG 5.8 0.2 - - - -
926B CYS* 1.3 80.9 - - - +
928B GLU* 1.3 61.6 + - - +
929B LYS* 4.1 1.0 + - - +
941B ARG* 5.9 0.4 - - - +
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Residues in contact with GLU 928 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862B GLU 3.5 8.0 - - - +
863B LEU* 3.9 20.7 + - + +
927B GLU* 1.3 73.5 - - - +
929B LYS* 1.3 63.6 + - - +
930B GLY 3.2 29.5 + - - +
931B ARG* 4.0 8.1 - - + +
932B CYS* 3.5 33.5 + - - +
939B CYS* 4.2 3.5 - - - +
941B ARG* 3.0 33.0 + - - +
944B LYS* 4.6 11.8 - - - +
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Residues in contact with LYS 929 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860B GLY 4.0 1.9 - - - +
861B SER* 3.3 2.8 - - - -
862B GLU* 2.8 59.0 + - + +
927B GLU 4.1 1.5 + - - +
928B GLU* 1.3 73.3 - - - +
930B GLY* 1.3 60.5 + - - +
952B VAL* 4.4 13.0 - - + -
953B LEU 4.4 14.3 + - - +
954B LEU* 4.1 25.6 + - + +
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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