Contacts of the helix formed by residues 118 - 131 (chain B) in PDB entry 5ZCJ
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 THR 118 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA* 3.6 1.6 - - - -
35B ALA 5.7 0.7 - - - +
117B LEU* 1.3 77.2 - - - +
119B LEU* 1.3 58.9 + - - +
120B GLU* 3.5 21.8 + - - +
121B GLN* 3.0 39.9 + - - +
122B LEU* 2.8 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA* 3.6 11.4 - - + +
35B ALA 3.9 13.4 + - - +
36B ASN* 3.6 35.0 - - + +
37B PRO* 4.2 13.9 - - + -
49B SER* 4.2 4.0 - - - +
118B THR* 1.3 73.9 - - - +
120B GLU* 1.3 68.2 + - - +
122B LEU* 3.3 20.2 + - + +
123B HIS* 2.9 28.3 + - + +
144B ARG* 3.9 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B THR* 3.6 18.0 + - - +
119B LEU* 1.3 88.4 + - - +
121B GLN* 1.3 61.0 + - + +
123B HIS* 3.3 7.1 + - - +
124B ALA* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.6 24.9 - - + +
118B THR* 3.0 45.8 + - - +
120B GLU* 1.3 73.9 - - + +
122B LEU* 1.3 65.9 + - - +
124B ALA* 3.1 10.0 + - + +
125B VAL* 3.0 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.9 1.3 - - + -
33B TYR 3.9 23.6 - - - +
34B ALA* 3.7 11.9 - - + -
49B SER* 3.4 36.3 - - - +
51B LEU* 3.5 39.0 - - + +
117B LEU* 3.7 23.5 - - + +
118B THR 2.8 20.7 + - - +
119B LEU* 3.5 10.8 - - + +
121B GLN* 1.3 72.2 - - - +
123B HIS* 1.3 60.7 + - - +
125B VAL* 3.1 7.3 + - - +
126B GLU* 3.1 24.3 + - - +
144B ARG* 4.8 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL 2.7 28.3 + - - -
131A HIS* 4.8 7.6 - - - -
135A HIS* 3.5 15.9 - + - -
119B LEU* 2.9 17.1 + - + +
120B GLU* 3.7 7.4 - - - +
122B LEU* 1.3 77.2 - - - +
124B ALA* 1.3 57.9 + - - +
126B GLU* 3.1 24.0 + - + -
127B ILE* 2.9 48.6 + - + +
144B ARG* 4.0 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B CYS* 4.2 6.7 - - - -
120B GLU 3.0 14.4 + - - +
121B GLN* 3.1 13.2 + - - +
123B HIS* 1.3 75.4 - - - +
125B VAL* 1.3 57.6 + - + +
127B ILE* 3.4 12.9 + - + +
128B SER* 2.9 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.1 11.4 - - + -
51B LEU* 3.8 22.2 - - + -
86B LEU* 4.2 24.6 - - + +
88B CYS* 4.0 19.7 - - - -
89B LEU* 4.3 15.3 - - + -
117B LEU* 4.1 20.2 - - + -
121B GLN* 3.0 18.7 + - + +
122B LEU 3.1 8.7 + - - +
124B ALA* 1.3 76.2 - - - +
126B GLU* 1.3 56.6 + - - +
128B SER* 3.1 2.1 + - - -
129B ALA* 2.8 28.2 + - - +
142B LEU* 4.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 4.5 10.2 - - + +
135A HIS* 2.7 36.1 + - + +
140A LEU 4.8 1.6 - - - +
51B LEU* 4.2 11.0 - - + +
122B LEU 3.1 10.1 + - - +
123B HIS* 3.1 17.2 + - + +
125B VAL* 1.3 77.4 - - - +
127B ILE* 1.3 62.1 + - - +
129B ALA* 3.3 9.7 + - - +
130B VAL* 3.4 14.4 + - - +
142B LEU* 4.3 26.7 - - + +
143B VAL 5.4 0.9 - - - -
144B ARG* 2.7 51.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 4.1 13.5 - - + -
131A HIS* 3.5 39.5 - - + +
123B HIS* 2.9 50.6 + - + +
124B ALA* 3.7 9.0 - - - +
126B GLU* 1.3 75.9 - - - +
128B SER* 1.3 61.5 + - - +
130B VAL* 3.2 7.3 - - - +
131B HIS* 3.0 37.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU 2.7 25.8 + - - +
87B GLY* 4.3 1.2 - - - -
88B CYS* 3.6 28.6 + - - +
124B ALA 2.9 17.8 + - - -
125B VAL 3.1 2.9 + - - -
127B ILE* 1.3 79.2 - - - +
129B ALA* 1.3 61.7 + - - +
131B HIS* 3.1 17.7 + - - +
132B SER* 3.2 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLY 3.6 20.8 - - - +
86B LEU* 3.9 7.2 + - + -
125B VAL 2.8 16.6 + - - +
126B GLU 3.3 3.5 + - - +
128B SER* 1.3 77.1 - - - +
130B VAL* 1.3 58.4 + - - +
132B SER* 2.7 25.7 + - - -
135B HIS* 3.5 9.6 + - - +
139B VAL* 6.3 0.2 - - + -
142B LEU* 3.6 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A HIS* 2.7 32.2 + - - +
126A GLU* 3.7 39.0 - - + +
127A ILE* 4.1 16.4 - - + +
130A VAL* 4.4 15.9 - - + -
126B GLU 3.4 8.1 + - - +
127B ILE* 3.2 20.0 - - - +
129B ALA* 1.3 78.7 - - - +
131B HIS* 1.3 68.1 + - + +
132B SER 3.4 0.4 - - - +
135B HIS* 3.6 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A HIS* 4.7 6.9 - - - -
127A ILE* 3.5 47.8 - - + +
131A HIS* 5.3 1.2 + - - -
127B ILE* 3.0 36.6 - - + +
128B SER* 3.1 11.2 + - - +
130B VAL* 1.3 78.7 - - + +
132B SER* 1.3 64.9 + - - +
----------------------------------------------------------
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