Contacts of the strand formed by residues 718 - 721 (chain C) in PDB entry 1GGE
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 ILE 718 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689C TYR* 3.9 6.3 - - + -
695C ILE* 3.4 24.2 - - + +
697C LEU* 4.5 19.5 - - + -
705C LYS* 5.0 2.0 - - + -
708C ILE* 3.8 19.7 - - + -
710C ILE* 4.1 19.5 - - + -
714C GLY* 5.7 0.3 - - - -
715C GLU* 3.0 39.7 + - + +
717C GLY* 1.3 86.0 + - - +
719C VAL* 1.3 71.9 + - - +
720C GLU* 3.8 21.6 + - + +
744C ARG* 3.7 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 719 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695C ILE 2.8 10.1 + - - +
696C ALA* 3.2 11.5 - - + -
697C LEU 2.8 26.0 + - - -
718C ILE* 1.3 76.9 - - - +
720C GLU* 1.3 65.1 + - - +
728C PHE* 3.6 42.4 - - + +
731C GLU* 3.8 25.1 - - + +
732C LEU* 3.9 19.1 - - + +
735C LEU* 3.4 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 720 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697C LEU* 3.4 11.7 - - + +
702C ARG* 4.0 19.6 + - + -
705C LYS* 2.7 45.2 + - + +
712C ASP 4.4 2.4 - - - +
713C GLN 5.6 0.2 - - - -
714C GLY* 3.5 20.2 - - - -
718C ILE* 3.8 18.2 + - + +
719C VAL* 1.3 80.9 - - - +
721C ALA* 1.3 68.2 + - - +
728C PHE* 4.3 3.6 - - - -
731C GLU* 5.0 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 721 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697C LEU 3.5 4.0 + - - -
698C ALA* 3.6 3.6 - - - -
699C GLY 2.9 22.3 + - - -
702C ARG* 3.4 15.4 + - - +
720C GLU* 1.3 80.4 - - - +
722C ASP* 1.3 62.2 + - - +
723C SER 3.3 18.1 + - - +
725C ASP 5.4 1.6 - - - +
728C PHE* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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