Contacts of the helix formed by residues 107 - 118 (chain A) in PDB entry 5WS3
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 CYS 107 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 3.1 16.1 + - - +
105A ILE 3.6 0.2 - - - -
106A THR* 1.3 95.2 - - - +
108A LEU* 1.3 67.4 + - - +
109A PRO* 3.4 2.0 - - - -
110A ALA* 3.3 4.9 + - - +
111A THR* 3.0 26.6 + - - +
130A ILE* 3.6 34.9 - - + +
133A LEU* 3.8 7.9 - - - -
134A GLN* 3.3 37.0 - - + +
354A TYR* 3.6 1.8 - - - +
2001A 7MA 5.7 0.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
61A TYR* 3.6 30.3 - - + +
64A VAL* 4.3 13.9 - - + -
65A PHE* 4.0 35.7 - - + +
103A VAL 2.9 10.5 + - - +
104A THR* 3.6 16.6 - - + +
107A CYS* 1.3 75.7 - - - +
109A PRO* 1.3 76.9 - - + +
111A THR* 3.2 2.4 + - - -
112A LEU* 2.9 23.7 + - + +
354A TYR* 3.7 39.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 4.8 8.5 - - + -
104A THR 3.6 12.6 - - - +
105A ILE 3.8 17.5 - - - +
106A THR 4.4 1.3 - - - -
107A CYS 3.6 4.5 - - - +
108A LEU* 1.3 103.2 - - + +
110A ALA* 1.3 61.9 + - - +
112A LEU* 3.3 8.1 + - + +
113A VAL* 3.0 31.3 + - + +
122A PHE* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A THR 4.7 2.4 + - - +
107A CYS 3.3 9.1 + - - +
108A LEU 3.3 0.6 - - - -
109A PRO* 1.3 79.4 - - - +
111A THR* 1.3 58.6 + - - +
113A VAL* 3.2 2.3 + - - +
114A VAL* 2.9 35.5 + - - +
120A TRP* 4.6 4.5 - - + -
122A PHE* 3.8 24.4 - - + -
130A ILE* 3.6 36.3 - - + -
2001A 7MA 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 3.6 13.0 - - - +
107A CYS 3.0 12.6 + - - -
108A LEU 3.6 3.6 - - - -
110A ALA* 1.3 75.9 - - - +
112A LEU* 1.3 59.1 + - - +
114A VAL* 3.9 4.2 - - - -
115A ASP* 2.9 51.7 + - - +
130A ILE* 5.4 0.2 - - - +
350A HIS* 4.0 5.4 - - + +
354A TYR* 2.9 23.8 + - + -
2001A 7MA 3.7 45.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 4.2 11.4 - - + +
58A ILE* 4.4 19.5 - - + +
61A TYR* 3.7 52.2 - - + -
62A ILE* 5.8 3.1 - - + -
108A LEU* 2.9 14.5 + - + +
109A PRO* 3.6 11.4 - - + +
111A THR* 1.3 76.3 - - - +
113A VAL* 1.3 67.8 + - + +
115A ASP* 3.3 2.6 + - - -
116A ILE* 2.9 52.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
109A PRO* 3.0 23.2 + - + +
110A ALA 3.2 4.2 + - - +
112A LEU* 1.3 79.3 - - + +
114A VAL* 1.3 58.9 + - - +
116A ILE* 3.3 6.0 + - + +
117A THR* 2.8 46.9 + - + +
119A THR 5.1 0.7 - - - +
121A PHE* 4.2 17.9 - - + -
122A PHE* 4.1 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ALA 2.9 21.3 + - - +
111A THR* 4.0 4.9 - - - +
113A VAL* 1.3 75.5 - - + +
115A ASP* 1.3 63.7 + - - +
117A THR* 4.0 5.2 - - - -
118A GLU* 2.7 31.8 + - - -
119A THR 3.9 20.2 - - - +
120A TRP* 3.5 35.9 - - + -
122A PHE* 4.6 5.8 - - + -
343A TYR* 3.1 7.1 + - - +
2001A 7MA 5.2 8.1 - - + -
2007A 1PE 4.3 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS* 3.5 7.3 - - - +
57A LEU* 4.5 10.7 - - + +
61A TYR* 3.7 6.2 + - - +
111A THR* 2.9 23.8 + - - +
112A LEU* 3.8 4.5 - - - +
114A VAL* 1.3 85.2 - - - +
116A ILE* 1.3 61.3 + - - +
343A TYR* 3.1 33.5 + - - -
347A THR* 3.7 24.5 - - + +
350A HIS* 2.7 46.4 + - - +
2007A 1PE 5.7 1.7 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
49A HIS 4.7 7.3 - - - +
50A PRO* 5.8 0.6 - - + +
51A LYS* 3.6 22.1 + - - +
54A GLU* 3.5 27.9 - - + +
57A LEU* 4.4 10.8 - - + -
58A ILE* 3.6 28.9 - - + -
112A LEU* 2.9 45.3 + - + +
113A VAL* 3.7 6.3 - - + +
115A ASP* 1.3 80.3 - - - +
117A THR* 1.3 72.3 + - + +
118A GLU* 3.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.8 33.2 - - + +
49A HIS 6.0 0.7 - - - -
113A VAL* 2.8 29.3 + - + +
116A ILE* 1.3 88.6 - - + +
118A GLU* 1.3 71.2 + - - +
119A THR* 3.2 36.3 + - - +
121A PHE* 3.5 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS* 2.5 34.7 + - - +
114A VAL* 2.7 27.2 + - - -
117A THR* 1.3 75.3 - - - +
119A THR* 1.3 63.5 + - + +
207A PHE* 5.0 1.6 - - - -
209A VAL* 3.9 16.5 - - - +
339A ARG* 3.1 31.5 + - - -
343A TYR* 3.3 31.8 - - + +
2007A 1PE 6.6 0.2 - - - -
----------------------------------------------------------
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