Contacts of the helix formed by residues 112 - 122 (chain A) in PDB entry 1UA4
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 112 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASN* 3.5 11.2 - - - -
32A ASN* 3.2 17.7 - - - +
111A GLY* 1.3 71.2 - - - -
113A GLN* 1.3 66.8 + - - -
114A ALA 3.3 2.7 - - - -
116A ILE* 2.9 29.8 + - - +
1457A GLC 2.9 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY 5.4 0.4 - - - +
30A ASN* 2.8 20.7 + - - +
112A GLY* 1.3 69.9 - - - -
114A ALA* 1.3 65.0 + - - +
116A ILE* 4.1 0.3 - - - +
117A MET* 3.0 38.7 + - + +
230A ILE* 6.2 0.2 - - + -
232A SER* 3.4 32.0 + - - +
235A GLN* 3.1 12.3 + - - +
266A GLU* 3.9 15.2 - - + +
267A PHE 5.6 0.2 + - - -
268A ALA* 5.0 6.6 - - - +
440A ASP* 2.8 33.5 + - - +
1457A GLC 2.6 45.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.0 9.7 - - - +
28A GLY* 3.7 38.1 + - - +
30A ASN* 3.0 16.2 + - - +
31A THR* 3.7 8.5 - - - +
113A GLN* 1.3 78.5 - - - +
115A GLY* 1.3 57.2 + - - +
117A MET* 3.8 2.2 - - - -
118A ALA* 2.9 31.5 + - - +
131A VAL* 3.8 12.7 - - + +
132A HIS 4.2 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASN 3.5 2.4 + - - -
31A THR* 3.4 15.1 + - - -
110A MET* 3.4 34.5 - - - +
111A GLY 3.9 2.5 - - - -
112A GLY 3.4 3.5 + - - -
113A GLN 3.4 0.6 - - - -
114A ALA* 1.3 79.8 - - - +
116A ILE* 1.3 61.5 + - - +
118A ALA* 3.3 2.9 + - - +
119A ASN* 3.1 19.2 + - - +
144A PHE* 4.2 7.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 4.6 2.0 - - - +
110A MET* 3.6 28.0 - - + +
111A GLY* 4.0 1.6 - - - -
112A GLY 2.9 18.5 + - - +
113A GLN 4.2 0.7 - - - +
115A GLY* 1.3 71.6 - - - +
117A MET* 1.3 63.3 + - - +
119A ASN* 3.4 5.5 + - - +
120A LEU* 3.1 22.8 + - + +
372A LYS* 5.1 11.4 - - - +
436A VAL* 5.3 1.3 - - + -
437A GLY* 4.0 17.5 - - - +
440A ASP* 3.6 33.9 - - + +
441A THR* 4.9 7.2 - - - +
1457A GLC 3.5 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.8 15.3 - - + -
113A GLN* 3.0 31.3 + - + +
114A ALA* 4.0 2.7 - - - +
116A ILE* 1.3 74.2 - - - +
118A ALA* 1.3 60.3 + - - +
120A LEU* 4.5 5.6 - - - -
121A LEU* 2.9 36.0 + - + +
230A ILE* 3.5 33.0 - - + -
266A GLU* 4.0 24.5 - - + +
440A ASP* 3.8 44.2 - - + +
443A SER* 4.7 0.4 - - - -
444A SER* 3.8 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.4 17.2 - - + +
114A ALA 2.9 19.1 + - - +
115A GLY 3.5 5.8 - - - +
116A ILE 3.2 0.2 - - - -
117A MET* 1.3 77.2 - - - +
119A ASN* 1.3 57.6 + - - +
122A GLY* 2.9 31.1 + - - +
123A GLY 3.5 0.9 + - - -
129A VAL* 4.0 9.8 - - + +
131A VAL* 4.0 13.2 - - + -
144A PHE* 4.0 19.1 - - + -
149A ILE* 3.7 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A MET* 3.4 23.2 - - - +
115A GLY 3.1 9.2 + - - +
116A ILE* 3.8 8.5 - - - +
118A ALA* 1.3 77.9 - - - +
120A LEU* 1.3 58.2 + - - +
123A GLY* 2.9 26.5 + - - -
124A VAL* 3.2 3.7 + - - +
143A LEU 3.0 23.2 + - - -
144A PHE* 3.3 14.0 - - - -
145A LEU* 2.9 46.3 + - + +
149A ILE* 3.7 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 3.1 17.7 + - + +
117A MET* 3.8 4.3 - - - +
119A ASN* 1.3 74.9 - - - +
121A LEU* 1.3 63.3 + - + +
124A VAL* 3.0 24.1 + - + +
125A TYR* 2.9 55.5 + - + +
378A ILE* 4.0 22.9 - - + -
440A ASP 5.3 0.2 - - - -
441A THR* 3.7 24.0 - - + +
444A SER* 3.6 22.7 - - - +
445A SER* 3.6 19.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
25A VAL* 4.1 21.5 - - + -
27A LEU* 4.3 13.9 - - + -
117A MET 2.9 22.8 + - - +
120A LEU* 1.3 74.2 - - + +
122A GLY* 1.3 57.6 + - - +
125A TYR* 3.2 34.3 - - + +
126A GLY 3.0 9.9 + - - -
127A VAL* 2.8 28.6 + - + +
129A VAL* 3.9 11.0 - - + -
230A ILE* 4.5 3.6 - - + -
444A SER* 4.4 19.3 - - - +
448A ILE* 3.8 43.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA 2.9 17.9 + - - -
121A LEU* 1.3 73.2 - - - +
123A GLY* 1.3 63.8 + - - +
126A GLY* 3.4 18.5 + - - -
127A VAL 3.0 18.1 + - - -
129A VAL* 4.0 4.3 - - - +
147A GLY* 4.6 0.2 - - - -
148A PRO* 3.5 17.0 - - - +
149A ILE* 4.1 13.5 - - - -
----------------------------------------------------------
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