Contacts of the strand formed by residues 119 - 125 (chain B) in PDB entry 3EE6
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 PHE 119 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B THR* 4.3 8.7 - - + -
51B PHE 3.6 5.2 - - - -
52B ALA* 4.0 19.5 - - + -
53B LEU* 4.7 3.2 - - - +
113B SER* 3.1 28.6 + - - -
114B VAL* 4.0 11.7 + - + +
116B THR* 4.8 0.2 - - - -
117B GLN* 3.3 1.3 - - - +
118B ASP* 1.3 97.8 + - - +
120B LEU* 1.3 62.8 + - - +
169B PHE* 5.2 0.2 - + - -
305B LEU* 4.2 23.1 - - + -
308B LEU* 5.4 0.9 - - + -
309B MET* 3.5 49.8 - - + -
312B SER* 5.5 1.1 - - - -
339B ARG* 3.2 26.7 - - + -
343B GLU* 3.3 39.3 - - + -
346B LYS* 4.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B THR* 3.2 1.7 - - - +
51B PHE* 2.6 52.8 + - + +
53B LEU* 4.6 11.9 - - + -
99B VAL* 4.3 12.8 - - + -
100B GLN* 4.9 16.2 - - + +
103B LEU* 4.1 19.3 - - + -
111B CYS* 3.9 13.7 - - + -
112B HIS* 3.2 27.6 - - - +
113B SER* 4.0 8.7 - - - +
119B PHE* 1.3 78.0 - - - +
121B THR* 1.3 61.0 - - - +
122B CYS* 4.2 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B SER* 3.2 26.0 - - - +
49B LEU 3.3 3.1 - - - +
50B THR* 3.1 24.0 + - - +
111B CYS* 3.2 22.9 - - - +
112B HIS* 3.4 27.9 + - + +
120B LEU* 1.3 72.3 - - - +
122B CYS* 1.3 62.6 + - - +
123B TRP* 6.2 1.6 - - + +
301B GLN* 4.0 10.5 - - - +
306B GLN* 4.2 7.2 + - - +
309B MET* 3.4 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU 3.5 0.5 - - - +
48B SER* 3.2 8.3 - - - -
49B LEU* 2.9 33.1 + - - +
51B PHE* 4.7 9.2 - - + -
103B LEU* 4.2 17.5 - - - -
108B ALA* 4.1 20.4 - - + -
109B GLN 3.9 1.1 - - - +
110B LYS 4.6 0.7 - - - -
111B CYS* 2.1 49.1 - - - +
120B LEU* 4.1 7.8 + - - -
121B THR* 1.3 73.0 - - - +
123B TRP* 1.3 66.8 + - - +
124B LEU* 4.1 4.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 4.0 18.8 - - + +
47B LEU* 3.2 47.8 - - - -
48B SER* 3.4 20.8 - - - -
108B ALA* 3.8 0.2 - - - -
109B GLN* 3.0 47.3 + - + +
110B LYS* 4.3 13.0 - - + +
112B HIS* 5.5 9.9 - + - -
121B THR* 6.2 1.2 - - + +
122B CYS* 1.3 76.8 - - - +
124B LEU* 1.3 62.8 - - - +
299B GLU* 4.5 25.1 - - + -
300B GLY 5.4 2.2 - - - -
301B GLN* 5.2 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 3.3 5.4 - - - -
47B LEU* 2.8 39.2 + - - +
49B LEU* 4.3 18.8 - - + -
51B PHE* 4.6 20.0 - - + -
103B LEU* 4.8 4.7 - - + -
106B ALA* 2.8 33.9 - - + +
108B ALA* 3.1 32.3 - - + +
122B CYS* 4.1 4.6 + - + -
123B TRP* 1.3 76.9 - - - +
125B SER* 1.3 69.2 + - - +
128B GLN* 3.5 12.3 - - + +
129B ALA* 4.3 15.5 - - + -
132B LEU* 5.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PRO 3.8 6.3 - - - -
44B GLU 4.1 4.3 - - - -
45B GLU 3.4 5.8 - - - -
46B GLU* 3.0 24.8 + - - -
124B LEU* 1.3 75.3 - - - +
126B ILE* 1.3 65.5 + - - +
127B ARG* 2.8 36.1 + - - -
128B GLN* 3.0 29.4 + - - +
129B ALA* 2.9 18.2 + - - +
----------------------------------------------------------
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