Contacts of the strand formed by residues 74 - 80 (chain u) in PDB entry 6QXT
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 PRO 74 (chain u).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66u ILE* 5.8 6.7 - - + -
67u PHE 3.6 11.2 - - - +
68u CYS* 4.2 4.7 - - + -
72u ARG 3.5 3.4 - - - -
73u LEU* 1.3 74.3 - - - +
75u THR* 1.3 60.2 + - - +
76u ALA 5.8 0.9 - - - +
189u ALA* 5.3 5.3 - - + +
190u ARG* 5.3 7.2 - - - -
193u VAL* 4.0 26.5 - - + -
81v TYR* 4.3 11.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67u PHE* 3.0 11.2 + - - -
68u CYS* 4.9 1.6 - - - -
69u ASP* 4.7 14.6 - - - -
73u LEU 3.3 5.5 + - - -
74u PRO* 1.3 72.3 - - - +
76u ALA* 1.3 56.9 + - - +
56v LYS* 5.7 4.9 - - - -
59v VAL* 4.4 18.2 - - - -
80v PRO* 3.4 4.1 - - - +
81v TYR* 2.5 39.8 + - - +
82v TYR 4.2 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66u ILE* 4.0 0.7 - - - -
67u PHE* 3.0 38.3 + - + +
74u PRO* 5.8 1.1 - - - +
75u THR* 1.3 80.0 - - - +
77u PHE* 1.3 62.0 + - - +
55v VAL 6.0 0.2 - - - +
59v VAL* 4.6 13.5 - - + -
78v LEU* 4.7 11.7 - - + -
79v THR 3.3 18.6 - - - +
80v PRO* 3.7 10.5 - - + -
81v TYR* 4.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64u LEU* 6.6 0.2 - - + -
65u VAL 3.4 14.6 - - - +
66u ILE* 4.8 4.3 - - + -
76u ALA* 1.3 76.2 - - - +
78u LEU* 1.3 66.3 + - - +
79u THR* 3.5 0.5 + - - -
78v LEU* 3.8 2.8 - - - -
79v THR* 2.9 35.9 + - - +
81v TYR 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63u ILE 5.9 0.7 - - - +
64u LEU* 5.7 2.4 - - - +
65u VAL* 3.1 37.8 + - + +
77u PHE* 1.3 74.9 - - - +
79u THR* 1.3 58.4 + - - +
80u PRO 4.0 2.0 - - - -
76v ALA* 4.9 10.8 - - + -
77v PHE 4.0 5.2 - - - +
78v LEU* 4.7 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 79 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77u PHE 3.5 0.4 + - - -
78u LEU* 1.3 73.1 - - - +
80u PRO* 1.3 65.3 - - - +
81u TYR 3.9 0.2 + - - -
76v ALA* 3.4 3.5 - - - -
77v PHE* 2.8 39.2 + - - +
79v THR* 4.3 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 80 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59u VAL* 5.0 15.7 - - + +
78u LEU 4.0 2.0 - - - -
79u THR* 1.3 77.1 - - - +
81u TYR* 1.3 63.5 + - - +
82u TYR 3.3 19.5 + - - +
83u ALA 5.0 5.4 - - - +
84u ARG* 5.1 11.6 - - - +
75v THR 3.8 2.5 - - - +
76v ALA* 3.7 16.4 - - + -
----------------------------------------------------------
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