Contacts of the strand formed by residues 106 - 114 (chain B) in PDB entry 6DBT
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 LEU 106 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 4.8 22.4 - - + -
92B ILE 3.9 5.6 - - - +
93B HIS* 3.9 13.1 - - + -
105B SER* 1.3 73.6 - - - +
107B TYR* 1.3 85.4 + - - +
108B MET* 4.5 3.6 - - + +
126B GLU* 3.9 2.6 - - - +
127B LYS* 3.4 57.3 + - + +
129B LEU* 3.8 37.6 - - + +
142B LEU* 5.8 5.6 - - + -
185B ILE* 4.5 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A ARG* 2.1 37.9 + - - -
67B SER* 5.2 0.9 - - - -
68B TYR 5.2 0.4 - - - -
69B LEU* 3.4 54.5 - - + -
70B PRO* 4.1 9.0 - - + +
72B LEU* 4.4 17.9 - - + -
91B LEU* 3.5 7.6 - - - +
92B ILE* 2.9 45.0 + - + +
103B SER* 4.4 2.7 - - - -
105B SER* 3.2 34.9 + - - -
106B LEU* 1.3 84.8 - - - +
108B MET* 1.3 61.3 + - - +
125B GLU 3.8 2.7 - - - +
126B GLU* 3.3 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 6.3 0.2 - - - -
80B PHE* 5.2 6.5 - - + -
89B CYS* 4.3 24.2 - - + -
90B TYR 3.8 3.1 - - - -
91B LEU* 3.8 20.6 - - + -
106B LEU* 5.1 4.0 - - + -
107B TYR* 1.3 76.1 - - - +
109B LEU* 1.3 62.7 + - - +
110B SER* 4.5 1.1 + - - -
123B ARG 4.1 0.3 - - - +
124B CYS* 3.4 5.1 - - - +
125B GLU* 2.9 51.3 + - + +
127B LYS* 3.6 37.0 - - + -
187B LEU* 5.1 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 3.9 23.1 - - + -
24B LEU* 4.6 19.8 - - + +
29B TYR* 5.8 1.6 - - + -
31B PHE* 5.3 2.2 - - + -
45B ILE* 3.9 19.7 - - + -
69B LEU* 5.7 2.9 - - + -
89B CYS* 3.2 7.8 - - - +
90B TYR* 2.9 42.9 + - + +
92B ILE* 4.7 14.1 - - + -
108B MET* 1.3 76.6 - - - +
110B SER* 1.3 75.3 - - - +
122B LEU* 4.8 16.4 - - + -
123B ARG 3.5 2.9 - - - +
124B CYS* 3.7 25.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 6.0 2.2 - - - -
86B LYS* 3.3 25.5 + - - -
87B PRO 4.6 2.9 + - - -
88B GLU 4.1 8.8 + - - -
89B CYS* 3.7 19.2 - - - -
108B MET* 5.6 2.0 - - - -
109B LEU* 1.3 84.2 - - - +
111B VAL* 1.3 81.5 + - - +
122B LEU* 3.7 7.1 - - - +
123B ARG* 2.9 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 4.7 12.5 - - + +
25B GLU* 4.7 17.7 - - + +
29B TYR* 5.2 0.7 - - - +
86B LYS* 4.0 10.2 + - - -
87B PRO 5.8 1.3 - - - +
88B GLU* 4.5 11.4 + - + +
110B SER* 1.3 88.3 + - - +
112B ASP* 1.3 64.8 + - - +
113B SER 4.5 6.1 - - - +
114B ARG* 4.6 21.3 - - - +
120B VAL* 3.9 13.5 - - + -
121B THR 3.4 14.6 - - - +
122B LEU* 3.6 15.9 - - + -
123B ARG* 5.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B SER* 5.4 9.0 - - - -
86B LYS* 5.5 4.8 + - - +
111B VAL* 1.3 79.5 - - - +
113B SER* 1.3 80.0 + - - +
114B ARG* 6.3 0.4 - - - -
121B THR* 2.9 25.3 + - - +
122B LEU 5.1 0.4 - - - +
123B ARG* 5.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B VAL* 4.5 4.2 - - - +
112B ASP* 1.3 95.0 + - - +
114B ARG* 1.3 71.4 + - - +
120B VAL* 4.1 2.4 - - - +
121B THR* 2.6 49.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLU* 4.1 37.0 + - - +
29B TYR* 5.6 3.2 + - - -
111B VAL* 4.6 20.5 - - - +
112B ASP 6.3 0.2 - - - -
113B SER* 1.3 83.0 - - - +
115B GLY* 1.3 65.9 + - - +
116B CYS* 4.0 0.4 - - - -
118B ARG* 5.8 2.9 - - - -
119B LYS 3.1 17.9 - - - +
120B VAL* 4.6 9.4 - - + +
121B THR* 4.8 0.6 - - - +
----------------------------------------------------------
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