Contacts of the strand formed by residues 7 - 13 (chain w) 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 ARG 7 (chain w).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6w MET* 1.3 71.6 - - - +
8w MET* 1.3 60.0 + - - +
9w ILE 3.7 0.6 + - - -
46w SER* 6.4 1.1 - - - -
47w LYS 4.0 3.8 - - - -
48w LEU* 4.8 4.9 - - + +
75w LEU 3.4 4.3 - - - +
76w THR* 3.5 2.6 - - - -
77w VAL* 2.6 60.4 + - + +
78w THR 4.5 7.6 - - - +
79w GLU* 5.1 1.8 - - - +
82w PHE* 4.8 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 8 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6w MET* 3.5 4.2 + - + +
7w ARG* 1.3 70.8 - - - +
9w ILE* 1.3 61.6 + - - +
10w LEU* 3.9 2.7 + - + +
46w SER* 3.0 8.4 - - - -
47w LYS* 2.9 50.0 + - + +
49w LEU* 5.3 7.6 - - + -
74w ILE* 6.3 2.5 - - + -
75w LEU 3.6 5.2 - - - +
76w THR* 5.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 9 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7w ARG 3.7 2.3 + - - +
8w MET* 1.3 73.3 - - - +
10w LEU* 1.3 59.5 + - - +
45w TYR 3.7 6.7 - - - +
46w SER* 4.4 4.7 - - - +
73w THR 3.4 1.0 - - - +
74w ILE* 3.3 5.9 - - - +
75w LEU* 2.9 47.7 + - + +
77w VAL* 5.5 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 10 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8w MET* 5.0 4.0 - - + +
9w ILE* 1.3 74.5 - - - +
11w MET* 1.3 62.4 + - - +
12w PHE* 5.7 0.2 - - - -
43w SER 3.5 1.4 - - - +
44w VAL* 4.0 0.9 - - - -
45w TYR* 2.9 50.4 + - + +
46w SER* 5.4 0.4 - - - -
72w ILE* 6.0 3.6 - - + -
73w THR 3.1 7.0 - - - +
74w ILE* 5.2 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 11 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9w ILE 4.3 0.2 - - - -
10w LEU* 1.3 73.3 - - - +
12w PHE* 1.3 61.7 + - - +
43w SER* 3.1 11.9 - - - +
44w VAL* 5.0 1.3 - - - +
71w ASN 4.4 0.4 - - - -
72w ILE* 3.1 9.4 - - - +
73w THR* 2.9 45.3 + - - -
44x VAL* 6.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 12 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10w LEU 5.6 0.4 - - - +
11w MET* 1.3 75.1 - - - +
13w ASP* 1.3 59.9 + - - +
43w SER* 3.1 36.5 + - - +
71w ASN 3.4 6.3 - - - +
72w ILE* 5.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 13 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12w PHE* 1.3 74.6 - - - +
14w MET* 1.3 64.4 + - - +
43w SER* 5.6 1.3 - - - -
70w GLY* 3.8 0.5 - - - -
71w ASN* 2.9 42.1 + - + +
42x PHE* 4.9 20.9 - - + +
43x SER* 5.9 3.1 - - - -
----------------------------------------------------------
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