Contacts of the helix formed by residues 108 - 117 (chain B) in PDB entry 3W1Y
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 108 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLU 3.3 25.4 - - - -
72B THR* 4.1 12.3 - - - +
73B ALA 3.8 8.7 - - - -
74B THR* 4.3 4.7 - - + +
106B SER 3.5 3.7 + - - +
107B ALA* 1.3 73.2 - - - +
109B LEU* 1.3 60.3 + - - +
110B GLY 3.7 4.0 - - - -
111B ASP* 3.2 30.0 + - - +
112B ILE* 3.1 29.1 + - - +
46C LYS* 4.3 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 3.6 13.6 - - + +
33B ILE* 4.2 9.0 - - + -
69B LEU* 4.0 26.7 - - + -
70B PRO 4.7 3.8 - - - +
73B ALA* 3.0 22.0 + - + +
74B THR 3.9 10.5 - - - +
75B VAL* 4.1 23.1 - - + -
78B PHE* 3.7 32.8 - - + -
98B ILE* 4.8 8.7 - - + -
108B CYS* 1.3 69.4 - - - +
110B GLY* 1.3 55.9 + - - +
112B ILE* 3.6 4.3 - - + +
113B TYR* 2.7 36.4 + - - +
123B LEU* 4.5 18.7 - - + +
125B VAL* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 3.3 19.2 - - - +
71B GLU* 3.2 21.7 + - - -
108B CYS 3.3 0.4 - - - -
109B LEU* 1.3 74.9 - - - +
111B ASP* 1.3 64.8 + - - +
113B TYR* 3.8 2.5 - - - +
114B ALA* 3.1 24.4 + - - +
46C LYS* 4.0 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B CYS* 3.2 33.0 + - + +
110B GLY* 1.3 77.7 - - - +
112B ILE* 1.3 62.0 + - - +
114B ALA* 3.4 14.5 + - - +
115B ARG* 3.5 34.8 + - - +
46C LYS* 4.3 11.2 + - - +
68C ARG* 3.0 35.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 3.7 30.1 - - + -
98B ILE* 3.7 33.2 - - + -
103B PRO* 3.8 18.2 - - + -
104B PRO* 5.1 0.9 - - + -
107B ALA* 3.8 12.1 - - + -
108B CYS 3.1 13.2 + - - +
109B LEU* 3.7 9.6 - - + +
111B ASP* 1.3 72.9 - - - +
113B TYR* 1.3 65.1 + - - +
115B ARG* 3.1 32.3 + - - +
116B ALA* 2.9 25.1 + - + +
123B LEU* 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 3.4 44.5 + - - -
31B ILE* 3.2 36.1 - - + -
32B PRO* 3.8 12.5 - - + +
109B LEU 2.7 21.9 + - - +
110B GLY* 3.8 3.4 - - - +
112B ILE* 1.3 72.9 - - - +
114B ALA* 1.3 62.0 + - - +
117B LYS* 3.0 66.2 + - + +
121B GLY* 2.6 34.9 + - - -
123B LEU* 3.9 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLY 3.1 17.5 + - - +
111B ASP* 3.7 7.6 - - - +
112B ILE 3.2 0.8 + - - -
113B TYR* 1.3 78.5 - - + +
115B ARG* 1.3 59.3 + - + +
117B LYS* 4.2 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PRO* 5.8 3.0 - - - +
107B ALA* 4.8 7.7 - - - +
111B ASP* 3.5 30.4 + - - +
112B ILE* 3.1 43.6 + - - +
114B ALA* 1.3 77.0 - - - +
116B ALA* 1.3 63.4 + - + +
117B LYS* 3.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ILE* 4.1 17.0 - - + +
112B ILE* 2.9 16.1 + - + +
115B ARG* 1.3 85.8 - - + +
117B LYS* 1.3 68.9 + - - +
118B ASP* 3.5 1.2 + - - -
123B LEU* 3.9 19.0 - - + +
124B TYR 5.4 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TYR* 3.0 64.8 + - + +
114B ALA* 4.2 16.4 - - - +
115B ARG 3.9 0.9 - - - -
116B ALA* 1.3 80.7 - - - +
118B ASP* 1.3 70.6 + - - +
119B PRO* 4.0 1.7 - - - +
121B GLY* 4.4 3.1 - - - +
122B PHE 3.6 6.7 - - - +
123B LEU* 4.2 6.7 - - - +
----------------------------------------------------------
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