Contacts of the helix formed by residues 103 - 114 (chain A) in PDB entry 3WF4
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 ASP 103 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 3.1 20.4 + - - +
65A TRP* 3.6 9.5 - - + -
98A PHE 3.1 19.7 - - - +
99A SER* 3.8 4.2 + - - -
100A GLU 3.3 19.7 + - - +
101A ASP 3.4 2.6 + - - -
102A HIS* 1.3 72.8 - - - +
104A VAL* 1.3 65.7 + - - +
105A GLU* 3.6 12.6 + - - +
106A TYR* 3.1 27.3 + - + +
107A PHE 3.1 17.7 + - - -
109A ARG* 4.9 4.4 + - - -
99B SER* 4.7 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 3.6 41.5 - - + +
84A VAL* 4.4 12.1 - - + -
89A HIS* 4.0 16.8 - - + +
98A PHE* 4.3 18.5 + - + -
102A HIS 3.1 3.2 + - - -
103A ASP* 1.3 74.2 - - - +
105A GLU* 1.3 66.7 + - + +
107A PHE* 3.4 4.8 + - - +
108A LEU* 3.0 41.8 + - + +
120A LEU* 5.0 1.1 - - + -
165A LEU* 4.6 6.3 - - + -
169A MET* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 4.5 10.0 - - - +
103A ASP* 3.1 10.3 + - - +
104A VAL* 1.3 78.6 - - + +
106A TYR* 1.3 57.9 + - - +
108A LEU* 3.2 4.7 + - - +
109A ARG* 2.9 44.9 + - - +
168A LYS* 3.2 47.9 - - + +
169A MET* 4.2 12.6 - - + -
172A LEU* 4.1 25.2 - - + +
105B GLU* 5.3 2.8 - - - +
168B LYS* 4.2 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 3.5 39.3 - - + -
65A TRP* 3.8 11.0 - + - -
103A ASP* 3.1 28.3 + - + +
105A GLU* 1.3 76.6 - - - +
107A PHE* 1.3 67.4 + - - +
109A ARG* 3.1 33.8 + - + +
110A LEU* 2.8 55.1 + - + +
113A GLU* 5.7 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 4.0 36.3 - - + -
57A TYR* 3.7 41.7 - + + -
65A TRP* 3.8 40.8 - + + -
69A LEU* 3.9 27.6 - - + -
80A ILE* 4.1 10.5 - - + -
82A THR* 4.0 16.8 - - + -
103A ASP 3.1 6.1 + - - +
104A VAL* 3.6 8.3 - - - +
106A TYR* 1.3 79.2 - - - +
108A LEU* 1.3 72.0 + - + +
110A LEU* 3.3 5.6 + - - +
111A ALA* 3.0 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A THR* 4.5 3.8 - - + -
104A VAL* 3.0 19.7 + - + +
105A GLU 3.7 6.1 - - - +
107A PHE* 1.3 98.3 - - + +
109A ARG* 1.3 59.6 + - - +
111A ALA* 3.5 4.3 + - - +
112A HIS 3.2 16.5 + - - -
118A VAL* 3.8 29.8 - - + -
120A LEU* 4.2 16.4 - - + -
169A MET* 3.6 31.4 - - + -
172A LEU* 4.0 20.2 - - + -
179A PRO* 3.5 19.1 - - + +
180A VAL* 4.4 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASP* 4.9 4.9 + - - -
105A GLU* 2.9 35.3 + - - +
106A TYR* 3.4 42.7 - - + +
108A LEU* 1.3 73.2 - - - +
110A LEU* 1.3 60.6 + - - +
112A HIS* 3.1 7.4 + - - +
113A GLU* 2.8 52.1 + - - +
172A LEU* 4.4 15.8 - - + +
96B TYR* 5.7 7.0 + - - +
98B PHE* 6.0 4.6 - - - +
99B SER* 5.0 8.7 + - - -
168B LYS* 6.0 2.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
62A ARG 5.6 0.2 - - - +
65A TRP* 3.7 18.4 - - + -
66A LYS* 3.7 57.7 - - + +
69A LEU* 3.9 7.9 - - + -
106A TYR* 2.8 48.4 + - + +
107A PHE 3.4 8.7 - - - +
109A ARG* 1.3 72.1 - - - +
111A ALA* 1.3 65.2 + - - +
113A GLU* 3.2 16.0 + - + +
114A LEU* 2.9 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.8 16.3 - - + +
80A ILE* 4.4 14.1 - - + -
107A PHE* 3.0 10.5 + - + +
108A LEU* 3.7 9.6 - - + +
110A LEU* 1.3 77.8 - - - +
112A HIS* 1.3 62.8 + - - +
114A LEU* 3.0 14.1 + - - +
116A LEU* 3.1 30.4 + - + +
118A VAL* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG* 4.0 12.6 + - - -
108A LEU 3.2 10.7 + - - +
109A ARG* 3.1 11.1 + - - +
111A ALA* 1.3 79.6 - - - +
113A GLU* 1.3 61.0 + - - +
115A GLY* 2.9 21.0 + - - -
116A LEU 3.8 9.8 + - - -
117A LEU* 5.7 3.6 - - + -
172A LEU* 6.3 0.2 - - + -
177A GLY 3.0 27.9 + - - -
178A GLY* 3.8 6.0 + - - -
179A PRO* 3.7 32.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 5.7 4.9 - - - -
109A ARG* 2.8 42.4 + - - +
110A LEU* 3.8 15.4 + - + +
112A HIS* 1.3 75.8 - - - +
114A LEU* 1.3 61.2 + - - +
115A GLY 3.2 1.6 + - - -
94B GLY 5.6 1.6 - - - +
95B GLN* 6.0 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LYS* 4.1 33.2 - - + +
69A LEU* 3.5 44.6 - - + +
70A LEU* 3.9 27.1 - - + +
73A LYS* 3.2 36.7 + - + +
110A LEU* 2.9 19.9 + - + +
111A ALA 3.0 7.8 + - - +
113A GLU* 1.3 77.6 - - - +
115A GLY* 1.3 59.8 + - - +
116A LEU* 3.3 9.8 + - + -
----------------------------------------------------------
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