Contacts of the strand formed by residues 112 - 117 (chain S) in PDB entry 3ALQ
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 112 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82S GLN* 4.0 13.2 + - - +
96S CYS* 2.9 27.7 + - - +
97S THR* 4.6 4.0 - - + -
98S CYS* 3.6 16.6 - - - -
104S CYS* 2.0 51.4 - - + -
106S LEU 4.2 0.2 - - - -
108S LYS* 4.2 9.8 + - - +
111S GLY* 1.3 73.7 - - - -
113S ARG* 1.3 60.8 + - - +
114S LEU 3.1 22.7 - - - -
115S CYS* 3.9 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 4.1 2.8 - - - +
115B TYR* 3.9 16.3 + - - +
143B ASP* 3.0 29.1 + - - -
145B ALA* 3.1 24.1 - - + +
146B GLU* 3.4 23.6 + - - +
149B GLN* 3.0 35.9 + - - +
95C SER* 5.8 0.2 + - - -
97C ILE* 3.1 34.2 - - - +
79S SER* 5.2 2.6 - - - -
82S GLN* 3.3 16.1 + - - -
106S LEU* 3.0 31.1 + - - +
107S SER 4.6 1.8 - - - +
108S LYS* 4.1 22.1 - - + +
112S CYS* 1.3 74.5 - - - +
114S LEU* 1.3 62.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLN* 4.4 15.3 - - - +
113B PRO* 3.6 35.9 - - + -
115B TYR* 4.4 16.8 - - - +
73C HIS* 5.9 3.6 - - + -
75C LEU* 3.6 27.1 - - + -
82S GLN* 4.7 0.2 - - - +
105S ALA* 2.8 37.9 + - + -
106S LEU* 3.3 17.4 + - + +
112S CYS* 3.1 9.9 - - - -
113S ARG* 1.3 82.1 - - + +
115S CYS* 1.3 74.0 + - - +
116S ALA* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 115 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLN* 5.2 4.3 + - - -
80S SER 5.3 2.0 - - - +
81S ASP* 4.3 8.1 - - + +
82S GLN* 3.9 25.5 - - + +
97S THR 4.3 0.4 - - - -
98S CYS* 2.0 57.0 - - + -
102S TRP* 3.9 20.9 - - + -
103S TYR 3.4 3.1 - - - +
112S CYS* 3.9 7.4 - - - -
113S ARG 4.3 0.2 - - - -
114S LEU* 1.3 87.7 - - - +
116S ALA* 1.3 61.4 + - - +
117S PRO* 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C HIS* 4.8 12.1 - - + -
102S TRP* 3.1 8.9 - - - -
103S TYR* 2.8 63.4 + - + +
105S ALA* 4.2 11.9 - - + -
114S LEU* 4.2 1.5 + - + -
115S CYS* 1.3 74.6 - - - +
117S PRO* 1.3 73.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 117 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C HIS* 6.2 1.1 - - + -
101S GLY 4.0 4.5 - - - +
102S TRP* 3.6 32.1 - - + -
103S TYR* 3.6 9.1 - - - -
115S CYS 4.7 0.2 - - - +
116S ALA* 1.3 89.0 - - + +
118S LEU* 1.3 68.3 + - - +
119S ARG* 3.3 3.6 + - - -
136S ASP* 4.4 0.5 - - - +
120U LYS* 6.1 3.6 - - - +
----------------------------------------------------------
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