Contacts of the helix formed by residues 117 - 127 (chain A) in PDB entry 2YZ5
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 HIS 117 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASP* 5.9 1.2 + - - -
49A SER* 5.4 7.9 + - - -
114A PRO* 3.0 31.3 + - + +
115A LEU 3.4 0.7 - - - +
116A ASP* 1.3 80.2 + - - +
118A PRO* 1.3 73.5 - - + +
119A ASP* 3.1 37.6 + - + -
120A HIS* 2.9 40.6 + + + +
121A GLN 3.3 8.5 + - - -
161A PHE* 3.8 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASP 3.3 9.6 - - - +
117A HIS* 1.3 94.3 - - + +
119A ASP* 1.3 67.5 + - - +
120A HIS 3.1 1.4 + - - -
121A GLN* 3.0 28.5 + - - +
160A LYS* 4.5 6.1 - - - +
161A PHE* 3.5 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A HIS* 3.1 26.9 + - + +
118A PRO* 1.3 82.0 - - - +
120A HIS* 1.3 76.8 + - + +
121A GLN* 3.7 0.4 - - - -
122A GLU* 5.4 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TRP* 3.6 22.7 + + + +
114A PRO* 4.0 15.5 - - + +
115A LEU 6.1 0.2 - - - -
117A HIS* 2.9 39.6 + + + +
119A ASP* 1.3 95.1 + - + +
121A GLN* 1.3 56.0 + - - +
122A GLU* 2.9 14.4 + - - +
123A GLU* 2.9 23.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU 5.5 0.4 - - - -
117A HIS 3.3 4.7 + - - -
118A PRO* 3.0 27.6 + - - +
119A ASP 5.2 0.2 - - - -
120A HIS* 1.3 76.3 - - - +
122A GLU* 1.3 63.5 + - + +
123A GLU 3.0 1.1 - - - -
124A TYR* 3.1 34.4 + - - +
161A PHE* 3.4 57.8 - - + +
163A HIS* 4.6 3.5 - - + -
198A PRO* 5.9 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASP 5.4 2.0 - - - +
120A HIS* 2.9 4.2 + - - +
121A GLN* 1.3 82.7 - - + +
123A GLU* 1.3 61.7 + - - +
124A TYR 3.0 0.4 - - - -
125A ALA* 3.1 23.2 + - - +
126A TRP* 3.7 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TRP* 3.4 36.3 - - + +
120A HIS* 2.9 15.9 + - + +
122A GLU* 1.3 78.5 - - - +
124A TYR* 1.3 62.4 + - - +
126A TRP* 3.0 31.1 + - - +
127A ARG* 2.9 45.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TRP* 3.6 25.1 - + - -
115A LEU* 2.9 35.9 + - - +
121A GLN* 3.1 27.2 + - + +
122A GLU 3.0 0.8 - - - -
123A GLU* 1.3 79.2 - - - +
125A ALA* 1.3 62.6 + - - +
126A TRP 3.1 1.0 + - - -
127A ARG* 3.2 23.1 + - + +
129A LEU* 4.3 12.6 - - + -
132A VAL* 4.3 16.8 - - + -
157A LEU 4.8 0.9 + - - -
158A PRO* 3.5 36.4 + - - +
160A LYS* 5.7 0.5 - - - +
161A PHE* 3.9 16.4 - + - -
163A HIS* 3.3 42.8 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU* 3.1 14.8 + - - +
123A GLU 3.1 1.2 - - - -
124A TYR* 1.3 77.6 - - - +
126A TRP* 1.3 65.6 + - + +
127A ARG 3.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU* 3.7 19.7 + - - +
123A GLU* 3.0 30.9 + - - +
125A ALA* 1.3 85.8 - - + +
127A ARG* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 5.0 12.7 + - - +
113A TRP* 3.6 44.6 - - + +
123A GLU* 2.9 46.2 + - + +
124A TYR* 3.2 17.4 + - + +
125A ALA 4.7 1.7 - - - +
126A TRP* 1.3 84.8 - - - +
128A ASP* 1.3 61.1 + - - +
129A LEU* 3.4 3.7 + - - +
132A VAL* 3.5 26.5 - - + +
----------------------------------------------------------
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