Contacts of the strand formed by residues 793 - 799 (chain B) in PDB entry 5GJE
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 793 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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751B ARG* 4.1 0.2 - - - +
765B THR* 3.0 34.3 + - + -
766B GLU 5.4 0.2 + - - -
767B TRP* 2.6 29.7 + - - +
772B LYS 5.6 0.4 - - - +
773B ILE* 4.3 10.8 - - + -
790B VAL* 4.4 4.0 - - + -
791B GLY 3.0 10.2 + - - +
792B ARG* 1.3 72.8 - - - +
794B ASN* 1.3 59.7 + - - +
807B TRP* 3.7 19.5 - - + +
808B THR 3.1 13.0 - - - +
809B ASP* 4.5 0.9 - - - +
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Residues in contact with ASN 794 (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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751B ARG* 3.0 40.0 + - - +
752B ALA* 4.2 5.3 - - - +
767B TRP* 4.3 4.5 - - + -
793B ALA* 1.3 75.2 - - - +
795B GLY* 1.3 76.2 + - - +
796B LEU 3.0 4.8 + - - +
807B TRP* 3.6 3.5 - - - +
808B THR* 3.0 39.9 + - - +
810B LEU* 3.8 11.9 - - + -
836B PHE* 3.0 48.9 + - - +
837B GLY* 4.4 2.0 - - - +
877B MET 4.7 1.6 + - - -
878B ASP* 6.4 0.2 - - - -
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Residues in contact with GLY 795 (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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752B ALA* 4.0 4.3 - - - +
794B ASN* 1.3 88.2 + - - +
796B LEU* 1.3 66.7 + - - +
797B THR* 3.0 20.0 + - - +
806B TYR 3.7 2.4 - - - +
836B PHE 4.6 0.2 - - - -
837B GLY* 5.0 0.7 - - - -
838B LEU* 3.6 31.4 - - - +
878B ASP* 5.2 7.6 - - - -
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Residues in contact with LEU 796 (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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752B ALA* 3.8 13.9 - - + +
753B LEU 4.4 4.9 - - - +
754B ALA* 3.5 22.5 - - + +
763B TYR* 3.7 43.3 - - + +
764B TRP* 3.7 16.6 - - - +
765B THR* 3.8 19.3 - - + +
773B ILE* 4.5 10.8 - - + -
794B ASN 3.0 4.0 + - - -
795B GLY* 1.3 73.5 - - - +
797B THR* 1.3 60.9 + - - +
805B LEU* 4.6 15.5 - - + -
806B TYR 3.5 15.7 - - - +
807B TRP* 4.1 20.6 - - + -
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Residues in contact with THR 797 (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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754B ALA* 4.6 1.1 - - - -
795B GLY 3.0 16.4 - - - +
796B LEU* 1.3 75.2 - - - +
798B ILE* 1.3 68.8 + - - +
799B ASP 4.1 0.3 + - - -
805B LEU* 3.6 3.4 - - - +
806B TYR* 2.9 43.3 + - + +
838B LEU* 3.9 13.7 - - + -
839B THR* 3.9 27.1 - - - -
840B GLN* 4.1 12.9 + - + +
886B ARG* 3.7 18.1 + - - +
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Residues in contact with ILE 798 (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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754B ALA* 3.9 17.9 - - + +
755B LEU 3.7 22.0 - - - +
756B ASP* 4.1 5.6 - - + -
763B TYR* 3.8 32.1 - - + -
797B THR* 1.3 77.5 + - - +
799B ASP* 1.3 64.9 + - - +
800B TYR* 3.3 38.3 + - + +
803B ARG* 4.9 0.9 - - - +
804B ARG 3.5 11.2 - - - +
805B LEU* 3.3 15.9 - - + -
820B MET* 3.6 20.0 - - + -
840B GLN* 4.8 0.9 - - - -
886B ARG* 3.3 22.3 + - - +
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Residues in contact with ASP 799 (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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797B THR 4.1 1.4 + - - -
798B ILE* 1.3 69.7 - - - +
800B TYR* 1.3 58.3 + - - +
801B ALA* 3.7 7.4 + - - +
802B LYS* 3.6 19.2 + - - +
803B ARG* 2.9 25.1 + - - -
804B ARG* 2.9 21.7 + - + +
806B TYR* 3.7 25.6 + - + -
840B GLN* 3.1 28.8 + - - +
860B LYS* 2.9 34.7 + - - +
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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