Contacts of the helix formed by residues 117 - 128 (chain A) in PDB entry 4UQJ
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 117 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PRO 3.3 4.7 + - - +
116A ASP* 1.3 71.2 + - - +
118A LYS* 1.3 65.8 + - - +
119A GLY 3.1 3.4 - - - -
120A ALA* 3.0 12.1 + - + +
121A LEU* 2.9 27.1 + - + +
145A THR* 5.3 7.6 - - + -
223A ALA* 3.5 38.6 - - + +
224A ASN* 3.5 14.8 - - - +
225A LEU* 3.8 24.0 - - + -
245A PHE* 3.6 39.9 - - + -
358A ILE* 4.2 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASP* 3.3 23.8 + - - +
117A LEU* 1.3 78.2 - - - +
119A GLY* 1.3 61.9 + - - +
121A LEU* 3.6 5.3 + - - +
122A LEU* 3.3 31.0 + - + +
144A SER* 5.5 3.4 - - - +
145A THR* 4.5 22.0 - - + +
148A ALA* 4.5 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASP* 4.2 5.9 + - - -
117A LEU 3.1 0.8 - - - -
118A LYS* 1.3 77.1 - - - +
120A ALA* 1.3 64.2 + - - +
122A LEU* 3.4 8.4 + - - +
123A SER* 3.1 26.2 + - - -
374A TRP* 3.5 23.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASP 4.7 0.2 + - - -
117A LEU* 3.0 18.6 + - + +
119A GLY* 1.3 75.5 - - - +
121A LEU* 1.3 61.2 + - - +
123A SER* 3.6 2.4 + - - -
124A LEU* 3.2 17.0 + - - +
245A PHE* 3.4 28.4 - - + -
358A ILE* 4.1 9.0 - - + -
374A TRP* 3.6 43.7 - - + +
380A MET* 4.6 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 2.9 19.5 + - + +
118A LYS* 3.8 6.1 - - - +
120A ALA* 1.3 74.5 - - - +
122A LEU* 1.3 67.5 + - + +
124A LEU* 3.0 13.3 + - + +
125A ILE* 3.1 36.6 + - + -
135A TYR* 4.5 20.6 - - + +
145A THR* 5.1 11.7 - - + -
149A VAL* 4.7 10.3 - - + -
193A ILE* 4.1 13.7 - - + -
195A ASP* 5.7 0.2 - - - -
221A ILE* 5.0 5.6 - - + -
223A ALA* 3.9 25.1 - - + -
245A PHE* 3.6 23.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LYS* 3.3 18.9 + - + +
119A GLY* 3.9 5.8 - - - +
121A LEU* 1.3 79.0 - - + +
123A SER* 1.3 62.0 + - - +
125A ILE* 3.4 9.7 + - + +
126A GLU* 3.4 26.1 + - - +
148A ALA* 4.2 13.2 - - + +
149A VAL* 3.9 35.4 - - + +
152A SER* 3.4 31.0 - - - +
158A TRP* 4.3 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLY 3.1 8.5 + - - -
120A ALA 3.8 1.1 - - - -
121A LEU 3.1 0.6 - - - -
122A LEU* 1.3 75.6 - - - +
124A LEU* 1.3 65.7 + - - +
126A GLU* 3.4 9.7 + - - +
127A TYR* 3.1 21.3 + - - +
374A TRP* 2.8 41.3 + - - -
379A LYS* 4.5 7.1 - - - +
380A MET* 4.1 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ALA 3.2 10.7 + - - +
121A LEU* 3.0 9.5 + - + +
123A SER* 1.3 75.8 - - - +
125A ILE* 1.3 65.9 + - - +
127A TYR* 3.1 13.5 + - + +
128A TYR* 3.2 54.2 + - + -
221A ILE* 3.9 24.2 - - + -
243A SER* 4.4 9.2 - - - -
244A GLY 4.8 5.6 - - - +
245A PHE* 3.6 24.5 - - + -
360A ILE* 3.8 18.4 - - + -
380A MET* 3.4 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 3.1 33.3 + - + +
122A LEU* 3.6 11.2 - - - +
124A LEU* 1.3 77.5 - - - +
126A GLU* 1.3 57.2 + - - +
128A TYR* 3.5 3.5 + - - +
129A GLN 3.1 20.6 + - - -
130A TRP* 3.1 39.7 + - + +
133A PHE* 3.7 20.9 - - + -
149A VAL* 4.6 7.6 - - + -
158A TRP* 3.7 32.8 - - + -
193A ILE* 3.7 22.9 - - + -
221A ILE* 5.0 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU 3.4 12.3 + - - +
123A SER* 3.4 10.7 + - - +
124A LEU 3.3 0.4 - - - -
125A ILE* 1.3 74.2 - - - +
127A TYR* 1.3 66.2 + - - +
129A GLN* 2.9 23.1 + - - +
130A TRP 5.0 0.4 - - - +
156A LYS* 4.8 8.1 - - - +
158A TRP* 4.1 22.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A SER 3.1 13.4 + - - +
124A LEU* 3.1 8.7 + - + +
126A GLU* 1.3 78.0 - - - +
128A TYR* 1.3 98.2 + + - +
129A GLN* 3.3 10.2 + - - +
362A GLU* 4.7 1.5 + - - -
371A ILE* 4.4 17.9 - - + +
380A MET* 3.8 25.6 - - + -
382A LEU* 3.5 41.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 3.2 50.9 + - + +
125A ILE* 3.5 1.1 + - - +
127A TYR* 1.3 93.1 - + - +
129A GLN* 1.3 72.2 + - - +
130A TRP* 3.2 27.9 - - + +
191A ARG* 4.5 4.9 + - - -
219A HIS* 3.8 25.6 - + - -
221A ILE* 4.4 8.7 - - + -
241A GLU* 5.2 2.7 - - - -
243A SER* 2.7 30.3 + - - -
360A ILE* 4.9 0.3 - - - +
362A GLU* 2.7 28.4 + - - +
371A ILE* 4.0 5.4 - - - +
----------------------------------------------------------
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