Contacts of the helix formed by residues 105 - 120 (chain A) in PDB entry 3UNE
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 PRO 105 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 3.8 24.5 - - + +
102A GLU* 5.8 4.0 - - - +
103A PRO 3.4 7.4 - - - +
104A ILE* 1.4 94.2 - - + +
106A THR* 1.3 65.0 + - - +
107A ALA* 3.3 4.9 - - + +
108A GLN* 3.1 30.6 + - + +
109A LEU* 3.1 11.6 + - - +
139A ASN* 3.5 19.1 - - + +
140A GLU* 5.2 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 4.4 11.5 - - + +
104A ILE 3.6 0.4 + - - -
105A PRO* 1.3 71.1 - - - +
107A ALA* 1.3 63.7 + - - +
108A GLN 3.3 0.7 + - - -
109A LEU* 3.3 2.9 + - - +
110A VAL* 3.1 28.1 + - - +
135A ILE* 4.0 16.4 - - + +
136A CYS 3.8 28.3 - - - +
137A GLY* 3.3 18.4 - - - +
139A ASN* 2.8 22.6 + - - +
144A TYR* 3.7 22.0 - - + +
146A PHE* 4.1 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PRO* 3.3 4.2 - - + -
106A THR* 1.3 79.5 - - - +
108A GLN* 1.3 62.0 + - + +
110A VAL* 4.3 2.9 - - - +
111A GLN* 3.3 31.8 + - - +
144A TYR* 5.1 10.6 - - + -
146A PHE* 3.7 28.7 - - + -
154A TYR* 5.3 0.9 - - - -
59B VAL* 5.6 3.1 - - + -
60B PHE* 4.5 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 5.1 6.3 - - + +
104A ILE* 4.3 2.5 - - + -
105A PRO* 3.1 35.6 + - + +
107A ALA* 1.3 80.5 - - + +
109A LEU* 1.3 63.1 + - - +
111A GLN* 3.5 37.3 + - - +
112A ARG* 3.3 56.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 4.1 12.6 - - + -
71A ILE* 3.7 39.3 - - + -
89A ALA* 3.5 28.9 - - + +
92A LEU* 4.3 8.7 - - + -
93A ALA* 3.8 14.6 - - + +
104A ILE* 3.8 24.0 - - + +
105A PRO 3.1 14.3 + - - +
106A THR 3.3 4.7 + - - +
108A GLN* 1.3 73.4 - - - +
110A VAL* 1.3 60.7 + - - +
112A ARG* 3.2 4.9 + - - +
113A VAL* 2.9 39.8 + - + +
135A ILE* 4.5 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A THR 3.1 17.9 + - - +
107A ALA 4.3 4.3 - - - +
108A GLN 3.4 0.2 - - - -
109A LEU* 1.3 74.4 - - - +
111A GLN* 1.3 56.9 + - - +
113A VAL* 3.9 5.8 - - + +
114A ALA* 2.9 30.3 + - - +
135A ILE* 3.8 39.0 - - + -
146A PHE* 3.7 34.8 - - + -
147A GLN 5.2 0.2 - - - +
148A SER* 4.5 7.0 - - - -
154A TYR* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ALA* 3.3 18.7 + - - +
108A GLN* 3.5 36.4 + - - +
109A LEU 3.3 0.2 - - - -
110A VAL* 1.3 78.8 - - - +
112A ARG* 1.3 59.5 + - + +
114A ALA* 4.2 1.4 - - - +
115A SER* 3.3 22.3 + - - -
154A TYR* 3.5 39.3 + - + +
60B PHE* 4.2 13.5 - - - -
91B ARG* 6.1 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 3.8 39.3 + - + +
96A TYR* 3.8 31.3 - - - +
100A TYR* 4.9 8.1 + - - -
104A ILE* 4.0 13.0 - - - +
108A GLN* 3.3 50.3 + - - +
109A LEU* 3.2 9.2 + - - +
111A GLN* 1.3 77.7 - - + +
113A VAL* 1.3 62.4 + - - +
115A SER* 3.5 7.3 + - - -
116A VAL* 3.4 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 6.0 1.8 - - + -
85A LEU* 4.6 13.7 - - + +
88A ARG* 6.3 1.3 - - + -
89A ALA* 3.8 32.5 - - + +
92A LEU* 4.5 8.3 - - + -
109A LEU* 2.9 29.1 + - + +
110A VAL* 3.9 6.7 - - + +
112A ARG* 1.3 75.9 - - - +
114A ALA* 1.3 62.6 + - - +
115A SER 3.2 0.2 - - - -
116A VAL* 3.2 8.8 + - + +
117A MET* 3.2 25.2 + - - +
133A LEU* 3.8 28.9 - - + -
135A ILE* 5.8 7.2 - - + -
148A SER* 5.2 2.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
110A VAL 2.9 18.4 + - - +
111A GLN 4.2 2.7 - - - +
113A VAL* 1.3 74.8 - - - +
115A SER* 1.3 59.2 + - - +
116A VAL 3.3 0.2 - - - -
117A MET* 3.3 6.7 + - - +
118A GLN* 2.9 29.1 + - - +
148A SER* 3.7 21.7 + - - +
152A GLY* 3.4 25.8 - - - +
154A TYR* 4.2 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN 3.3 19.0 + - - -
112A ARG* 3.6 10.5 - - - -
113A VAL 3.2 0.4 - - - -
114A ALA* 1.3 78.0 - - - +
116A VAL* 1.3 61.5 + - - +
118A GLN* 3.5 9.4 + - - +
119A GLU* 3.3 28.9 + - - +
85B VAL* 5.0 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 5.1 5.4 - - + -
88A ARG* 3.5 58.3 - - + +
92A LEU* 4.3 7.6 - - + -
112A ARG 3.4 16.6 - - - +
113A VAL* 3.2 8.9 + - + +
115A SER* 1.3 77.2 - - - +
117A MET* 1.3 62.3 + - + +
119A GLU* 3.2 21.6 + - - +
120A TYR* 3.3 29.1 - - + -
129A PHE* 4.8 7.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
85A LEU* 3.8 22.2 - - + -
113A VAL* 3.2 14.5 + - - +
114A ALA* 3.3 8.5 + - - +
116A VAL* 1.3 75.4 - - - +
118A GLN* 1.3 61.9 + - - +
119A GLU 3.6 0.2 + - - -
120A TYR* 3.8 7.5 + - - +
121A THR* 3.6 18.0 + - - +
128A PRO* 5.5 0.3 - - - +
129A PHE* 4.0 25.3 - - + -
131A VAL 3.4 25.4 - - - +
133A LEU* 3.8 20.9 - - + -
148A SER* 3.4 25.6 - - - +
149A ASP 3.5 20.6 - - - +
150A PRO* 3.7 12.9 - - + +
152A GLY* 4.4 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ALA 2.9 17.1 + - - +
115A SER* 3.6 11.1 - - - +
116A VAL 3.2 0.2 - - - -
117A MET* 1.3 76.8 - - - +
119A GLU* 1.3 70.2 + - - +
121A THR* 2.6 24.9 + - - +
122A GLN* 3.4 26.2 + - - +
151A SER 4.1 7.2 - - - +
152A GLY* 4.4 0.6 - - - +
81B SER* 3.6 33.9 - - - +
82B ASP* 2.8 28.2 + - - +
85B VAL* 3.4 23.8 - - + +
128B ARG* 3.6 4.8 - - - +
130B PHE* 4.7 0.8 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
88A ARG* 4.7 12.2 + - - -
115A SER* 3.3 17.5 + - - +
116A VAL* 3.2 19.4 + - - +
118A GLN* 1.3 84.5 + - - +
120A TYR* 1.3 62.0 + - + +
122A GLN* 2.9 5.6 + - - -
123A SER* 2.7 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 5.7 4.9 - - - +
88A ARG* 5.0 8.2 + - - -
116A VAL* 3.3 34.2 + - + -
117A MET 3.8 4.2 + - - +
118A GLN 3.3 0.8 - - - -
119A GLU* 1.3 84.6 - - + +
121A THR* 1.3 58.9 - - - +
122A GLN 3.4 0.4 - - - -
123A SER* 4.6 0.4 - - - -
126A VAL* 3.4 51.1 - - + +
127A ARG 3.4 18.1 - - - +
128A PRO* 3.3 24.4 - - + +
129A PHE* 3.5 34.5 - + + -
----------------------------------------------------------
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