Contacts of the helix formed by residues 111 - 127 (chain A) in PDB entry 4UTX
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 ASN 111 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 2.8 25.3 + - - +
60A GLU* 3.5 24.3 - - + +
61A SER* 2.7 31.0 + - - +
109A MET 4.4 0.2 - - - -
110A PRO* 1.3 76.7 - - - +
112A PRO* 1.3 76.4 - - + +
113A ALA* 2.9 37.5 + - - +
114A HIS* 3.2 21.3 + - - +
115A LEU* 3.4 14.5 + - - +
290A GLY* 4.6 0.7 - - - -
110B PRO 5.4 0.4 - - - -
112B PRO* 5.7 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASN* 1.3 92.3 - - + +
113A ALA* 1.3 57.7 + - - +
114A HIS 3.3 0.2 - - - -
115A LEU* 3.3 3.6 + - + +
116A ALA* 2.9 30.5 + - - +
290A GLY* 3.5 26.7 - - - +
294A PRO* 4.0 8.6 - - + +
109B MET* 3.8 24.5 - - + +
110B PRO 5.0 5.4 - - - +
111B ASN* 6.0 2.2 - - - -
112B PRO* 6.0 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 5.1 8.3 - - + -
111A ASN* 2.9 12.1 + - - +
112A PRO* 1.3 75.5 - - - +
114A HIS* 1.3 68.2 + - - +
115A LEU 3.1 0.7 + - - -
116A ALA* 3.3 4.0 + - - +
117A ILE* 3.1 32.5 + - + +
244A VAL* 5.3 0.9 - - + -
289A CYS* 3.8 39.0 - - + -
290A GLY* 4.1 2.0 - - - -
293A LEU* 3.9 16.7 - - + +
294A PRO* 4.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 3.2 30.3 - - + +
58A SER* 4.4 2.6 + - - -
61A SER* 3.5 7.4 - - - -
110A PRO* 3.7 18.3 - - + +
111A ASN* 3.2 49.7 + - - +
113A ALA* 1.3 79.6 - - - +
115A LEU* 1.3 58.2 + - - +
117A ILE* 3.6 6.5 - - - +
118A ALA* 3.1 20.4 + - - +
139A ASP* 5.0 0.4 + - - -
141A LEU* 3.5 33.8 - - + +
142A HIS* 3.6 33.2 + + - -
145A ALA* 3.6 14.6 - - + +
147A SER* 4.5 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO* 4.3 3.1 - - + +
111A ASN 3.4 20.1 + - - +
112A PRO* 3.3 6.5 + - + +
113A ALA 3.0 1.0 - - - -
114A HIS* 1.3 77.1 - - - +
116A ALA* 1.3 60.3 + - - +
117A ILE 3.0 1.3 - - - -
118A ALA* 2.7 22.3 + - - +
119A GLU* 2.7 27.2 + - + +
145A ALA* 3.9 29.6 - - + +
109B MET* 3.5 20.2 - - + -
110B PRO* 3.6 39.0 - - + +
115B LEU* 3.8 22.9 - - + -
144B ARG 4.7 7.4 - - - +
1301B DMS 4.8 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PRO 2.9 18.5 + - - +
113A ALA* 3.8 5.2 - - - +
115A LEU* 1.3 75.9 - - - +
117A ILE* 1.3 55.2 + - - +
119A GLU* 3.5 1.8 + - - +
120A CYS* 2.9 29.6 + - - +
123A ARG* 5.2 1.0 + - - -
293A LEU* 4.8 0.9 - - + -
294A PRO* 3.8 33.2 - - + -
297A LEU* 4.1 16.1 - - + +
109B MET* 3.5 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 4.1 30.7 - - + -
53A THR* 4.7 3.6 - - + -
57A VAL* 6.3 0.7 - - + -
113A ALA* 3.1 17.7 + - + +
114A HIS 3.6 5.6 - - - +
115A LEU 3.0 0.4 - - - -
116A ALA* 1.3 77.5 - - - +
118A ALA* 1.3 58.3 + - - +
120A CYS* 2.9 9.6 + - - +
121A GLU* 2.9 27.2 + - - +
131A VAL* 5.0 1.3 - - + +
133A ILE* 3.8 25.8 - - + -
142A HIS* 4.1 23.3 - - + +
147A SER* 3.8 13.7 - - - +
244A VAL* 5.2 3.6 - - + -
293A LEU* 3.9 22.4 - - + -
297A LEU* 4.2 8.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
114A HIS 3.1 9.0 + - - +
115A LEU 2.7 13.3 + - - +
117A ILE* 1.3 76.0 - - - +
119A GLU* 1.3 62.8 + - + +
121A GLU* 3.5 4.2 + - - +
122A ALA* 3.2 21.8 + - - +
145A ALA* 3.2 27.8 - - + +
146A GLY 3.6 18.3 - - - +
147A SER* 3.3 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 2.7 28.2 + - + +
116A ALA* 4.1 3.1 - - - +
118A ALA* 1.3 74.1 - - + +
120A CYS* 1.3 55.4 + - - +
122A ALA* 3.1 7.1 + - - +
123A ARG* 2.7 48.0 + - - +
145A ALA 5.7 0.4 - - - +
106B ARG 5.4 0.9 - - - +
109B MET* 2.9 18.6 - - + +
110B PRO* 4.7 0.7 - - - +
144B ARG* 2.7 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 4.1 31.9 - - - -
49A ILE* 5.4 2.0 - - - -
51A ILE* 5.8 2.7 - - + -
116A ALA 2.9 16.4 + - - +
117A ILE* 2.9 14.0 + - - +
119A GLU* 1.3 76.2 - - - +
121A GLU* 1.3 63.2 + - - +
123A ARG* 3.1 18.0 + - - +
124A LEU* 2.8 42.8 + - - +
131A VAL* 4.5 10.5 - - + -
297A LEU* 4.4 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE 2.9 12.2 + - - +
118A ALA* 3.7 3.8 - - - +
120A CYS* 1.3 75.3 - - - +
122A ALA* 1.3 55.4 + - - +
124A LEU* 3.7 0.7 - - - +
125A GLY* 2.7 34.1 + - - -
129A ARG 5.1 0.2 - - - +
131A VAL* 3.7 41.7 + - + +
133A ILE* 3.6 7.6 - - - +
146A GLY 5.0 0.9 - - - -
147A SER* 3.2 26.5 + - - -
148A LYS* 2.9 26.2 + - + +
149A HIS* 2.9 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA 3.2 11.5 + - - +
119A GLU* 3.1 11.6 + - - +
120A CYS 3.1 0.2 - - - -
121A GLU* 1.3 80.8 - - - +
123A ARG* 1.3 65.5 + - - +
125A GLY* 3.0 11.0 + - - -
126A GLN* 3.2 17.2 + - - +
146A GLY 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 4.5 4.0 - - - -
116A ALA 5.2 1.0 + - - -
119A GLU* 2.7 43.6 + - - +
120A CYS* 3.6 18.3 - - - +
122A ALA* 1.3 74.9 - - - +
124A LEU* 1.3 69.2 + - + +
126A GLN* 3.3 18.1 + - - +
127A GLN* 3.5 25.2 + - - +
297A LEU* 2.6 31.7 + - - +
298A GLU* 4.0 9.6 + - - +
106B ARG* 4.3 25.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
43A PHE* 4.5 8.1 - - + -
46A ALA 5.0 0.7 - - - +
49A ILE* 4.2 16.4 - - + -
120A CYS* 2.8 36.7 + - - +
121A GLU 4.1 1.8 - - - +
123A ARG* 1.3 88.5 - - + +
125A GLY* 1.3 65.9 + - - +
127A GLN* 3.0 19.9 + - - +
129A ARG* 2.9 75.5 + - + +
131A VAL* 3.9 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU 2.7 19.4 + - - -
122A ALA 3.0 2.6 + - - -
124A LEU* 1.3 75.8 - - - +
126A GLN* 1.3 57.7 + - - +
128A GLY* 2.9 20.1 + - - -
129A ARG 3.4 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ALA 3.2 12.8 + - - +
123A ARG* 3.5 11.2 - - - +
124A LEU 3.2 0.2 - - - -
125A GLY* 1.3 76.6 - - - +
127A GLN* 1.3 58.4 + - + +
128A GLY 3.2 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ARG* 3.6 33.7 + - - +
124A LEU* 3.0 14.5 + - - +
126A GLN* 1.3 75.6 - - + +
128A GLY* 1.3 60.7 + - - +
129A ARG* 2.9 41.7 + - - +
----------------------------------------------------------
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