Contacts of the strand formed by residues 799 - 807 (chain I) in PDB entry 4XLN
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 799 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G LEU 5.8 0.2 - - - +
63G HIS* 4.8 10.8 - - + -
65G PHE* 3.5 31.6 - - + -
746I GLY* 4.1 16.6 - - - +
747I ALA 3.1 20.2 - - - +
748I GLU* 4.5 8.3 + - - +
798I GLY* 1.3 77.3 - - - +
800I VAL* 1.3 64.4 + - - +
801I VAL* 3.6 21.8 - - + +
827I VAL* 3.4 8.0 - - - +
828I ALA* 3.3 37.3 + - + +
829I GLN* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 800 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G HIS* 3.8 1.1 - - - -
743I VAL* 3.7 43.3 - - + +
744I ARG 3.9 11.2 - - - +
745I ILE* 3.2 13.1 - - - +
746I GLY* 2.7 28.8 + - - +
747I ALA 4.1 2.1 + - - +
749I VAL* 4.1 9.9 - - + -
799I ILE* 1.3 82.7 - - - +
801I VAL* 1.3 58.7 + - - +
802I GLY* 3.3 29.6 - - - +
803I ARG* 5.2 1.8 - - + -
825I VAL* 3.7 15.5 - - + -
826I PHE 3.4 7.4 - - - +
827I VAL* 4.4 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 801 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G HIS* 3.5 25.3 + - + +
65G PHE* 3.9 19.5 - - + -
66G SER* 5.9 0.2 - - - -
628I TYR* 4.7 15.0 - - + +
705I ILE* 5.3 7.2 - - + -
745I ILE* 3.8 11.8 - - - +
799I ILE* 3.6 23.8 - - + +
800I VAL* 1.3 73.1 - - - +
802I GLY* 1.3 57.7 + - - +
826I PHE* 3.4 10.4 + - + +
828I ALA* 3.6 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 802 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745I ILE* 5.2 3.8 - - - -
800I VAL* 3.3 14.4 - - - +
801I VAL* 1.3 81.3 - - - +
803I ARG* 1.3 60.3 + - - +
825I VAL* 3.8 0.7 - - - -
826I PHE* 2.9 46.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 803 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738I ASP* 4.8 1.0 + - - -
740I GLU* 4.1 11.3 + - - -
742I ILE* 3.5 53.1 - - + +
743I VAL 4.3 13.2 + - - +
744I ARG* 4.7 3.8 - - - +
745I ILE* 4.6 19.6 - - + +
800I VAL* 5.2 2.2 - - + -
802I GLY* 1.3 76.3 - - - +
804I LEU* 1.3 70.8 + - - +
805I ARG* 4.1 10.3 + - + +
823I VAL* 4.7 9.4 - - + -
824I ARG 3.8 5.2 - - - +
825I VAL* 4.7 7.6 - - + +
826I PHE* 4.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 804 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I GLU* 3.6 46.9 - - + +
803I ARG* 1.3 78.3 - - - +
805I ARG* 1.3 61.9 + - - +
806I LEU* 3.9 16.3 + - + +
822I VAL 4.0 0.3 - - - +
823I VAL* 3.6 5.6 - - - +
824I ARG* 2.9 70.5 + - + +
826I PHE* 5.4 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 805 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722I ILE* 3.6 31.9 + - - +
740I GLU* 4.5 32.8 + - - +
742I ILE* 4.6 7.1 - - - +
803I ARG* 4.1 14.8 + - + +
804I LEU* 1.3 74.5 - - - +
806I LEU* 1.3 75.3 + - - +
807I ARG* 3.4 37.8 + - + +
810I ASP* 5.3 3.0 - - - +
821I GLU* 3.0 28.8 + - - -
822I VAL 4.2 1.3 - - - -
823I VAL* 3.9 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 806 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I GLU 3.9 22.2 - - - +
86I LYS* 4.8 12.1 - - + +
87I ASP* 5.4 1.3 - - - +
804I LEU* 3.9 17.2 + - + -
805I ARG* 1.3 84.2 - - - +
807I ARG* 1.3 58.3 + - - +
810I ASP* 5.5 0.7 - - + -
813I VAL* 4.2 37.9 - - + -
815I LEU* 3.7 2.1 - - - +
821I GLU* 3.9 0.6 - - - -
822I VAL* 2.8 58.5 + - + +
824I ARG* 5.5 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 807 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721I ARG* 5.5 5.3 - - - +
805I ARG* 3.4 32.5 - - + +
806I LEU* 1.3 73.7 - - - +
808I ARG* 1.3 70.4 + - - +
810I ASP* 3.2 54.4 + - - +
813I VAL* 4.3 5.2 - - - +
815I LEU* 4.2 2.0 - - - -
820I ARG* 3.8 12.6 - - - +
821I GLU* 3.4 37.2 + - + +
----------------------------------------------------------
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