Contacts of the helix formed by residues 110 - 117 (chain B) in PDB entry 5Z7R
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 110 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLY* 4.8 3.1 - - - -
109B LEU* 1.3 66.4 - - - +
111B GLY* 1.3 54.8 + - - -
112B GLY 2.8 4.5 + - - -
113B CYS* 2.8 24.1 + - - +
114B GLU* 3.0 18.6 + - - +
131B GLY 3.0 11.7 + - - -
132B GLN* 4.0 3.5 - - - +
133B PRO* 3.6 13.6 - - - +
134B GLU* 3.0 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.5 23.9 - - - +
63B VAL* 4.6 0.2 - - - -
65B GLY* 4.5 8.1 - - - -
66B ALA* 4.9 3.3 - - - +
90B PHE* 3.8 1.2 - - - -
109B LEU 3.4 1.2 + - - -
110B GLY* 1.3 69.4 - - - -
112B GLY* 1.3 55.6 + - - +
114B GLU* 3.1 20.0 + - - +
115B ILE* 3.1 27.9 + - - +
134B GLU* 3.7 2.0 + - - -
143B PHE* 4.0 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 3.5 10.6 - - - -
63B VAL* 3.5 40.2 - - - +
65B GLY* 4.6 0.6 - - - -
108B ALA* 4.0 6.9 - - - +
109B LEU 2.9 6.2 + - - -
110B GLY 2.8 4.0 + - - -
111B GLY* 1.3 72.7 - - - +
113B CYS* 1.3 66.2 + - - +
115B ILE* 3.5 5.3 - - - +
116B ALA* 3.2 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA* 3.3 27.1 - - - +
110B GLY 2.8 8.8 + - - +
112B GLY* 1.3 71.6 - - - -
114B GLU* 1.3 63.6 + - - +
116B ALA* 3.1 6.3 + - - +
117B MET* 2.9 42.4 + - - +
130B PHE* 4.1 20.0 - - - -
131B GLY 3.5 16.4 - - - +
132B GLN* 3.3 25.8 - - - +
149B LEU* 5.3 3.6 - - - -
178B LEU* 4.8 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE* 3.9 3.3 - - + -
110B GLY 3.0 6.2 + - - +
111B GLY* 3.1 29.9 + - - +
113B CYS* 1.3 78.1 - - - +
115B ILE* 1.3 57.1 + - - +
117B MET* 3.5 11.5 + - + +
118B SER* 2.9 25.1 + - - -
132B GLN* 3.8 17.3 - - - +
134B GLU* 3.5 5.9 - - - +
141B PRO* 3.3 2.8 - - - +
142B GLY 3.1 9.5 + - - -
143B PHE* 2.7 49.8 + - + +
144B GLY 4.4 0.2 - - - -
145B GLY* 2.9 34.4 + - - +
148B ARG* 4.6 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 5.3 3.4 - - + -
28B LEU* 4.7 12.3 - - + -
36B MET* 4.5 22.7 - - + -
54B LEU* 3.8 24.0 - - + -
62B PHE* 4.0 13.7 - - + -
63B VAL* 4.4 9.0 - - + -
90B PHE* 3.4 44.8 - - + -
93B LEU* 4.2 9.2 - - + -
111B GLY 3.1 13.1 + - - +
112B GLY* 3.5 15.5 - - - +
114B GLU* 1.3 73.3 - - - +
116B ALA* 1.3 68.0 + - - +
118B SER* 3.1 14.5 + - - -
119B CYS* 3.6 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 3.8 17.9 - - + -
102B ALA* 4.2 10.8 - - + -
104B VAL* 4.2 15.5 - - + -
112B GLY 3.2 9.6 + - - +
113B CYS* 3.1 10.9 + - - +
115B ILE* 1.3 79.1 - - - +
117B MET* 1.3 59.5 + - + +
118B SER 3.0 6.3 + - - -
119B CYS* 3.2 10.5 + - - +
122B ARG* 3.1 30.4 + - + +
130B PHE* 4.6 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU* 4.4 2.6 - - - +
113B CYS* 2.9 21.8 + - - +
114B GLU* 3.6 22.2 - - + +
115B ILE 3.3 0.2 - - - -
116B ALA* 1.3 75.5 - - - +
118B SER* 1.3 60.2 + - - +
119B CYS 3.3 6.5 + - - +
122B ARG* 3.8 11.7 + - - +
130B PHE* 6.5 0.4 - - + -
132B GLN* 3.3 30.3 - - - +
145B GLY* 4.1 8.1 - - - -
148B ARG* 3.4 21.7 - - + -
149B LEU* 3.4 50.0 - - + +
152B LEU* 3.8 21.6 - - + +
178B LEU* 4.1 13.7 - - + -
----------------------------------------------------------
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