Contacts of the helix formed by residues 123 - 132 (chain A) in PDB entry 5DST
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 GLY 123 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A SER* 2.9 19.1 + - - -
121A GLY 2.9 2.8 - - - -
122A THR* 1.3 77.4 - - - +
124A ILE* 1.3 65.2 + - - +
125A LEU 3.2 3.1 - - - -
126A SER* 3.0 14.2 + - - -
127A MET* 2.9 28.8 + - - +
149A SER* 4.2 7.6 - - - -
153A ILE* 4.8 9.4 - - - +
164A ILE* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 3.8 23.3 - - + -
95A ARG* 4.8 2.7 - - - +
96A THR* 4.5 2.7 - - + -
122A THR* 3.4 7.1 - - - +
123A GLY* 1.3 77.0 - - - +
125A LEU* 1.3 71.1 + - + +
127A MET* 3.2 10.3 + - + +
128A PHE* 3.1 47.5 + - + -
401A SAH 3.5 33.0 - - - +
242B VAL* 3.9 15.9 - - + +
243B TYR* 4.4 1.3 - - + -
245B PHE* 3.7 30.1 - - + -
247B MET* 4.1 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ARG* 5.6 3.4 - - - +
96A THR* 5.6 1.6 - - + -
99A TYR* 3.7 45.5 - - + -
103A MET* 3.9 3.2 - - + +
117A ASP* 3.4 18.8 + - - +
120A SER 4.9 0.6 + - - -
123A GLY 3.2 1.0 - - - -
124A ILE* 1.3 84.8 - - + +
126A SER* 1.3 62.6 + - - +
128A PHE* 3.2 21.9 + - + +
129A ALA 3.1 18.0 + - - -
183A ILE* 3.6 16.9 - - + +
184A SER* 4.3 4.9 - - - +
185A GLU* 3.9 21.5 - - + +
401A SAH 3.6 35.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASP* 2.8 37.3 + - - +
120A SER* 4.5 1.6 - - - -
123A GLY* 3.0 12.0 + - - -
125A LEU* 1.3 77.1 - - - +
127A MET* 1.3 55.3 + - - +
129A ALA* 3.4 2.6 + - - +
130A ALA* 3.0 23.6 + - - +
137A VAL* 3.6 22.2 - - - +
139A GLY* 4.2 7.6 - - - -
153A ILE* 5.3 0.4 - - - -
162A ILE* 3.5 26.6 - - - +
164A ILE* 5.2 1.6 - - - -
183A ILE* 4.4 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLY 2.9 13.6 + - - +
124A ILE* 3.6 21.5 - - - +
125A LEU 3.2 0.2 - - - -
126A SER* 1.3 74.1 - - - +
128A PHE* 1.3 64.0 + - - +
130A ALA* 3.5 1.7 + - - +
131A LYS* 3.0 27.7 + - - +
152A ILE* 3.9 21.1 - - + -
153A ILE* 4.1 12.8 - - + -
156A ASN* 3.7 17.7 - - - -
158A LEU* 3.8 14.9 - - + +
162A ILE* 3.8 15.5 - - + -
245B PHE* 3.4 57.0 - - + -
247B MET* 4.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A THR* 3.8 28.5 - - + -
99A TYR 4.4 1.3 - - - -
100A ARG* 3.4 53.4 - - + -
103A MET* 3.7 14.6 - - + -
104A TYR* 3.5 20.1 - - + -
124A ILE* 3.1 36.4 + - + -
125A LEU* 3.2 24.0 + - + +
127A MET* 1.3 75.9 - - - +
129A ALA* 1.3 57.9 + - - +
131A LYS 3.0 2.4 + - - -
132A ALA* 2.9 26.5 + - - +
243B TYR* 4.0 9.4 - + + -
245B PHE* 3.6 27.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A MET* 3.5 16.9 - - - -
110A PHE* 4.5 5.1 - - + +
115A VAL* 4.2 15.3 - - + -
125A LEU 3.1 10.3 + - - +
126A SER* 3.6 7.9 - - - +
128A PHE* 1.3 79.5 - - - +
130A ALA* 1.3 62.7 + - - +
132A ALA* 3.1 15.3 + - - +
133A GLY 3.3 1.0 + - - -
134A ALA* 3.3 17.8 + - - +
137A VAL* 4.0 13.5 - - + -
183A ILE* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A SER 3.0 17.0 + - - +
127A MET 3.7 4.3 - - - +
129A ALA* 1.3 74.6 - - - +
131A LYS* 1.3 59.2 + - - +
133A GLY* 2.9 22.0 + - - -
134A ALA 3.7 4.7 + - - +
137A VAL* 4.0 6.6 - - - +
158A LEU* 4.2 18.2 - - + -
161A ILE* 3.8 32.4 - - + +
162A ILE* 3.9 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A TYR* 3.5 30.9 - - + +
107A LYS* 4.1 12.3 - - - -
127A MET 3.0 17.4 + - - +
128A PHE 3.0 2.4 + - - +
130A ALA* 1.3 77.1 - - - +
132A ALA* 1.3 58.3 + - - +
133A GLY* 3.2 1.6 + - - -
156A ASN 5.4 3.8 + - - -
158A LEU* 4.7 20.2 - - + +
245B PHE* 4.1 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A MET* 3.6 36.8 - - + +
104A TYR* 4.4 2.4 - - + +
107A LYS* 3.4 32.5 - - + +
110A PHE* 3.6 24.4 - - + +
111A LYS* 4.1 1.6 + - - +
128A PHE 2.9 11.3 + - - +
129A ALA 3.1 10.0 + - - +
131A LYS* 1.3 76.0 - - - +
133A GLY* 1.3 56.3 + - - +
134A ALA 3.7 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