Contacts of the helix formed by residues 108 - 115 (chain H) in PDB entry 3SHD
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 SER 108 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H GLY 4.4 6.1 - - - -
17H LYS* 4.1 17.8 - - - +
18H PHE* 4.3 1.1 - - - -
107H VAL* 1.3 79.3 - - - +
109H ALA* 1.3 64.2 + - - +
110H GLU* 3.3 17.0 + - - +
111H GLU* 2.7 45.1 + - - +
112H ILE* 3.0 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H GLY 4.9 2.0 + - - -
18H PHE* 3.7 29.1 - - + -
108H SER* 1.3 72.7 - - - +
110H GLU* 1.3 79.7 + - - +
112H ILE* 3.1 3.9 + - - +
113H LEU* 2.9 27.7 + - + +
127H ILE* 4.1 7.8 - - + +
131H GLN* 3.3 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H SER* 3.3 14.6 + - - +
109H ALA* 1.3 94.6 + - - +
111H GLU* 1.3 63.2 + - - +
113H LEU* 3.4 11.9 + - + +
114H GLN* 3.1 34.1 + - + +
131H GLN* 4.8 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H LYS* 4.6 6.6 + - - -
31H TRP* 4.9 10.3 - - + -
106H TRP 5.1 0.3 - - - +
107H VAL* 3.7 21.4 - - + +
108H SER* 2.7 51.4 + - - +
110H GLU* 1.3 79.7 - - - +
112H ILE* 1.3 63.5 + - - +
114H GLN* 2.9 12.5 + - - +
115H ALA* 3.2 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H PHE* 3.9 17.5 - - + -
20H VAL* 3.6 28.7 - - + -
31H TRP* 4.5 6.3 - - + -
107H VAL* 3.2 24.4 - - + +
108H SER 3.0 9.4 + - - +
109H ALA 3.7 5.8 - - - +
111H GLU* 1.3 69.8 - - - +
113H LEU* 1.3 61.8 + - - +
114H GLN 3.4 0.5 + - - -
115H ALA* 3.5 11.0 + - - +
118H LEU* 3.4 32.7 - - + +
123H VAL* 4.3 15.5 - - + +
124H ALA* 4.4 5.6 - - - -
127H ILE* 3.7 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H ALA 2.9 24.2 + - - +
110H GLU* 3.7 10.1 - - + +
111H GLU 3.1 0.4 + - - -
112H ILE* 1.3 78.5 - - - +
114H GLN* 1.3 70.8 + - - +
115H ALA 4.7 1.9 - - - +
118H LEU* 5.1 1.4 - - - +
124H ALA* 3.6 41.4 - - + +
127H ILE* 3.8 16.8 - - + -
128H ARG* 4.2 27.1 + - + +
131H GLN* 3.9 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 114 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H GLU* 3.1 23.7 - - + +
111H GLU* 2.9 6.6 + - - +
113H LEU* 1.3 85.7 - - - +
115H ALA* 1.3 69.9 + - - +
116H SER* 3.5 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H TRP* 4.3 13.2 - - + -
111H GLU 3.2 10.1 + - - +
112H ILE 3.5 5.6 + - - +
113H LEU 4.7 1.0 - - - +
114H GLN* 1.3 81.1 - - - +
116H SER* 1.3 59.2 - - - +
117H ASN* 3.4 18.8 - - - +
118H LEU* 3.6 38.1 - - + +
----------------------------------------------------------
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