Contacts of the helix formed by residues 107 - 119 (chain A) in PDB entry 1YOB
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 107 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR 5.4 0.2 - - - +
56A THR* 3.3 7.6 - - - -
95A GLY* 3.6 12.8 - - - +
96A LEU 3.2 36.1 - - - +
97A GLY 3.5 4.3 - - - +
105A ASN 3.0 0.2 + - - -
106A TYR* 1.3 94.0 - - + +
108A ASP* 1.3 66.3 + - - +
109A ALA 3.1 3.1 - - - -
110A LEU* 2.9 35.0 + - + +
138A SER* 4.1 0.4 - - - +
140A ALA* 3.3 15.5 - - + +
146A PHE* 4.1 7.9 - - + -
150A ALA* 3.5 38.4 - - + -
151A LEU 4.1 0.2 - - - +
1200A FMN 2.8 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 3.4 1.6 + - - -
60A GLY* 3.5 19.9 - - - +
104A GLU 4.2 1.6 - - - +
105A ASN* 2.8 43.6 + - - +
107A LEU* 1.3 76.2 - - - +
109A ALA* 1.3 58.0 + - - +
111A GLY* 2.8 19.2 + - - -
112A GLU* 3.1 11.1 + - - +
138A SER* 3.7 7.8 - - - -
139A GLU* 2.8 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 4.2 2.9 - - + +
55A PRO 3.2 21.5 - - - +
56A THR* 3.0 24.1 + - - +
60A GLY 4.4 1.3 + - - -
61A GLU 3.7 12.6 - - - +
62A LEU* 3.4 30.4 - - + +
108A ASP* 1.3 77.8 - - - +
110A LEU* 1.3 56.1 + - - +
112A GLU* 3.2 6.2 + - - +
113A LEU* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 4.3 10.6 + - + +
56A THR* 4.2 0.6 + - - -
93A LEU* 3.7 32.1 - - + -
94A PHE 4.3 1.1 - - - +
95A GLY* 3.6 31.4 - - - +
107A LEU* 2.9 40.1 + - + +
109A ALA* 1.3 78.7 - - - +
111A GLY* 1.3 55.9 + - - +
113A LEU* 3.3 3.0 + - + +
114A TYR* 2.9 26.3 + - - +
140A ALA* 3.8 10.5 - - + -
146A PHE* 5.3 0.7 - - + -
147A VAL* 3.8 13.2 - - + -
148A GLY* 3.9 16.2 - - - +
149A LEU 3.8 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU 3.4 3.6 + - - -
108A ASP 2.8 10.0 + - - -
110A LEU* 1.3 79.3 - - - +
112A GLU* 1.3 59.9 + - - -
114A TYR* 3.1 11.8 - - - +
115A SER* 3.1 25.7 + - - -
139A GLU* 3.3 26.9 - - - -
140A ALA* 3.7 7.2 - - - +
147A VAL* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLY 5.3 1.2 - - - +
61A GLU* 4.9 3.8 - - - +
62A LEU* 3.5 40.2 + - + +
78A LEU* 5.1 5.0 - - + +
108A ASP 3.1 10.0 + - - +
109A ALA* 3.6 9.0 - - - +
111A GLY* 1.3 74.8 - - - +
113A LEU* 1.3 61.9 + - - +
115A SER* 3.4 7.8 + - - -
116A PHE* 3.1 21.8 + - - +
139A GLU* 5.5 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 4.4 6.1 - - + +
53A GLY 4.8 0.2 - - - +
54A THR* 3.5 25.4 - - + -
62A LEU* 4.2 11.6 - - + +
74A TRP* 3.7 50.5 - - + -
78A LEU* 4.2 15.3 - - + -
93A LEU* 4.0 24.4 - - + +
109A ALA 2.9 14.8 + - - +
110A LEU* 3.7 6.1 - - + +
112A GLU* 1.3 75.2 - - - +
114A TYR* 1.3 67.3 + - - +
116A PHE* 3.4 7.3 + - + +
117A PHE* 3.2 33.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 3.4 13.2 - - + +
110A LEU 2.9 13.3 + - - +
111A GLY* 3.1 11.0 - - - +
113A LEU* 1.3 78.3 - - - +
115A SER* 1.3 70.1 + - - +
117A PHE* 3.4 0.3 + - - -
118A LYS* 2.7 62.7 + - + +
124A ILE* 3.6 41.4 - - + +
139A GLU 5.8 0.7 - - - -
142A VAL* 4.1 22.3 - - + +
147A VAL* 3.5 45.8 - - + +
----------------------------------------------------------
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 GLY 3.1 10.7 + - - -
112A GLU* 3.8 9.8 - - - -
113A LEU 3.4 0.2 - - - -
114A TYR* 1.3 85.4 - - - +
116A PHE* 1.3 59.2 + - - +
118A LYS* 4.0 6.3 - - - -
119A ASP* 2.7 48.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.4 39.7 - - + -
81A ILE* 3.5 40.4 - - + -
82A GLU* 3.6 9.0 - - + -
86A PHE* 4.2 4.7 - + - -
112A GLU 3.1 13.9 + - - +
113A LEU* 3.5 11.9 - - - +
114A TYR 3.3 0.2 - - - -
115A SER* 1.3 79.3 - - - +
117A PHE* 1.3 88.3 + + + +
119A ASP* 3.8 2.8 - - - +
120A ARG* 3.0 69.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 4.0 15.9 - + - -
50A LEU* 4.7 1.3 - - + -
52A LEU* 3.3 34.3 - - + -
74A TRP* 4.5 4.7 - + - -
81A ILE* 4.0 6.1 - - + -
86A PHE* 3.7 44.9 - + - -
91A VAL* 4.5 14.8 - - + -
93A LEU* 4.8 3.8 - - + -
113A LEU* 3.2 36.6 - - + +
114A TYR* 3.4 3.9 + - - +
115A SER 3.3 0.2 - - - -
116A PHE* 1.3 99.7 - + - +
118A LYS* 1.3 67.0 + - - +
119A ASP 3.2 0.4 - - - -
120A ARG* 2.9 14.9 + - - +
122A ALA* 3.3 29.4 + - + +
124A ILE* 4.7 5.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
114A TYR* 2.7 51.3 + - + +
115A SER* 3.8 6.3 - - - +
117A PHE* 1.3 72.0 - - - +
119A ASP* 1.3 66.6 + - - +
120A ARG 3.1 1.4 + - - -
121A GLY* 3.1 14.2 + - - -
122A ALA 4.2 11.7 + - - +
123A LYS* 6.0 0.2 - - - +
124A ILE* 3.5 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER* 2.7 37.4 + - - +
116A PHE* 3.8 5.3 - - - +
118A LYS* 1.3 76.6 - - - +
120A ARG* 1.3 68.4 + - - +
121A GLY 3.3 1.8 + - - -
----------------------------------------------------------
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