Contacts of the strand formed by residues 106 - 114 (chain B) in PDB entry 5ELI
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 GLY 106 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG* 4.3 6.7 - - - -
105B ALA* 1.3 77.2 - - - +
107B LEU* 1.3 61.1 + - - -
108B TYR* 3.8 6.5 - - - -
125B LEU* 3.4 8.8 - - - +
126B VAL* 2.9 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B THR* 4.5 9.0 - - + +
52B ARG* 3.4 7.0 - - - +
53B GLN* 2.9 71.4 + - + +
55B GLY 5.4 1.8 - - - +
106B GLY* 1.3 72.7 - - - -
108B TYR* 1.3 66.0 + - - +
123B LYS* 4.4 15.3 - - + +
124B VAL 3.4 23.3 - - - +
125B LEU* 3.6 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TRP* 3.3 51.4 - + + -
51B CYS 3.2 13.0 - - - +
52B ARG* 3.1 57.7 + - + +
53B GLN* 5.1 1.3 - - - -
63B VAL* 4.5 6.7 - - + -
97B LEU* 5.5 6.3 - - + +
104B ASP* 2.2 37.4 + - - +
106B GLY 3.8 11.2 - - - -
107B LEU* 1.3 75.9 - - - +
109B GLN* 1.3 62.8 + - - +
123B LYS* 3.2 7.0 - - - +
124B VAL* 3.0 31.6 + - - +
126B VAL* 3.3 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA 3.8 0.5 - - - +
50B TRP* 3.6 7.2 - - - -
51B CYS* 2.9 34.9 + - - -
53B GLN* 3.0 31.3 + - + +
57B LYS 5.8 1.6 + - - -
60B CYS* 3.5 25.4 - - - +
108B TYR* 1.3 76.9 - - - +
110B CYS* 1.3 65.1 + - - +
111B GLN* 3.2 22.7 + - + +
120B THR* 2.5 33.0 + - + +
122B ARG 3.1 14.4 - - - +
123B LYS* 3.9 13.1 - - + +
124B VAL* 4.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B CYS* 2.1 51.1 - - + -
49B ALA 3.5 5.4 - - - -
50B TRP* 3.9 24.0 - - - +
93B LEU* 3.9 16.8 - - + -
95B ILE* 4.7 2.0 - - - -
109B GLN* 1.3 73.6 - - - +
111B GLN* 1.3 63.3 + - - +
120B THR* 3.5 4.2 - - - +
121B LEU* 2.9 31.9 + - + -
122B ARG* 2.8 12.5 + - - +
124B VAL* 5.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LYS* 3.0 9.5 - - - +
49B ALA* 2.9 39.3 + - + +
51B CYS* 3.3 33.3 - - - +
60B CYS* 4.2 7.3 - - - +
62B ARG* 4.6 5.4 + - - -
93B LEU* 5.1 0.2 - - - +
109B GLN* 3.2 25.0 + - - +
110B CYS* 1.3 80.4 - - - +
112B SER* 1.3 59.8 + - - +
113B LEU* 3.8 16.7 - - + +
118B ALA* 3.7 22.2 + - + +
119B ASP 3.1 10.8 - - - +
120B THR* 4.7 1.4 + - - -
121B LEU* 3.6 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B HIS* 3.0 27.7 + - - +
46B ARG* 3.0 35.5 - - - +
47B ARG 3.5 4.6 + - - -
48B LYS* 4.1 3.1 - - - +
111B GLN* 1.3 71.0 - - - +
113B LEU* 1.3 62.0 + - - +
114B HIS* 4.0 4.4 + - - -
118B ALA* 3.4 1.4 - - - -
119B ASP* 2.8 37.2 + - - +
121B LEU* 3.5 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ARG* 3.4 20.8 - - - +
47B ARG* 2.9 42.1 + - + +
48B LYS 4.2 7.6 - - - +
49B ALA* 3.7 25.6 - - + -
62B ARG* 3.6 36.3 - - - +
111B GLN* 3.8 8.3 - - + +
112B SER* 1.3 78.1 - - - +
114B HIS* 1.3 61.8 + - - +
115B GLY 5.3 3.1 - - - +
117B GLU 3.7 5.4 - - - +
118B ALA* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ARG* 3.0 45.3 + - + +
112B SER 4.1 2.2 + - - -
113B LEU* 1.3 76.0 - - - +
115B GLY* 1.3 67.5 + - - +
116B SER 3.4 0.2 + - - -
117B GLU* 2.9 42.9 + - + +
119B ASP* 3.0 46.6 + - - -
----------------------------------------------------------
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