Contacts of the helix formed by residues 134 - 146 (chain A) in PDB entry 6DU2
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 134 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ARG 3.4 0.2 + - - -
133A PRO* 1.3 93.9 - - + +
135A VAL* 1.3 64.1 + - - +
136A ASP 3.3 2.9 - - - +
137A GLU* 3.6 25.9 + - - +
138A PHE* 3.0 23.3 + - - +
231A ASP 3.7 10.1 + - - -
232A THR* 3.8 29.3 - - + +
234A LEU* 4.6 1.1 - - - -
235A HIS* 3.8 28.7 + + + +
238A LEU* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.9 45.1 - - + +
131A LYS* 3.7 35.9 - - + -
132A ARG 3.1 18.6 + - - +
133A PRO 3.2 0.2 - - - -
134A HIS* 1.3 78.4 - - - +
136A ASP* 1.3 63.3 + - - +
138A PHE* 3.1 0.8 + - - +
139A LEU* 2.8 37.3 + - + +
166A LEU* 4.1 13.5 - - + -
234A LEU* 3.9 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LYS* 2.9 39.3 + - - -
134A HIS 3.3 0.8 - - - -
135A VAL* 1.3 76.6 - - - +
137A GLU* 1.3 65.4 + - - +
140A GLN* 3.0 28.5 + - - +
166A LEU* 4.4 8.1 - - - +
168A LYS* 5.9 0.7 - - - +
169A TRP* 3.4 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A HIS* 3.6 25.2 + - - +
135A VAL 3.4 0.2 - - - -
136A ASP* 1.3 76.9 - - - +
138A PHE* 1.3 62.1 + - - +
140A GLN* 4.1 7.1 - - - +
141A ARG* 3.2 24.7 + - + +
235A HIS* 3.2 35.2 + - - +
238A LEU* 3.7 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 4.6 5.2 - - + -
101A LEU* 4.0 15.5 - - + -
134A HIS 3.0 19.2 + - - +
135A VAL* 3.1 5.4 + - - +
137A GLU* 1.3 78.9 - - - +
139A LEU* 1.3 74.0 + - + +
141A ARG* 4.0 1.2 - - - +
142A MET* 2.9 69.4 + - + +
205A LEU* 3.6 33.0 - - + -
234A LEU* 3.4 44.6 - - + +
235A HIS* 6.1 0.2 - - - -
237A LEU* 4.7 2.7 - - + -
238A LEU* 4.1 15.5 - - + -
241A PHE* 4.1 17.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 5.2 4.7 - - + -
101A LEU* 3.8 35.0 - - + -
135A VAL* 2.8 25.3 + - + +
138A PHE* 1.3 78.5 - - + +
140A GLN* 1.3 65.9 + - - +
142A MET* 3.9 3.9 - - + +
143A GLY 2.9 20.1 + - - -
166A LEU* 4.3 20.9 - - + +
167A ASP* 4.3 19.7 - - + +
169A TRP* 4.0 12.3 - - + -
171A ALA* 3.5 16.9 - - + +
172A PHE* 3.8 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ASP 3.0 18.2 + - - +
137A GLU* 4.1 6.1 - - - +
139A LEU* 1.3 79.0 - - - +
141A ARG* 1.3 76.2 + - - +
143A GLY* 3.5 1.7 + - - -
144A GLU* 2.8 48.7 + - - +
169A TRP* 3.5 50.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLU* 3.2 17.5 + - + +
140A GLN* 1.3 86.9 + - - +
142A MET* 1.3 58.2 + - - +
144A GLU* 2.7 58.5 + - - +
145A LEU* 3.1 31.6 + - + +
238A LEU* 3.7 26.0 - - + -
242A GLU* 2.6 43.9 + - - +
246A ARG* 4.1 8.9 - - - +
126B GLN* 3.9 14.5 + - - -
128B TYR* 4.6 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL* 3.7 20.6 - - + -
95A ILE* 4.2 10.3 - - + -
138A PHE* 2.9 59.3 + - + +
139A LEU* 3.9 5.4 - - + +
141A ARG* 1.3 75.5 - - - +
143A GLY* 1.3 57.8 + - - +
145A LEU* 4.4 3.6 - - - +
146A PHE* 3.0 61.2 + - + +
148A CYS* 3.2 18.7 - - - -
205A LEU* 5.4 0.4 - - + -
238A LEU* 4.6 5.8 - - + -
241A PHE* 3.7 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LYS* 3.2 14.0 + - - -
139A LEU 2.9 11.8 + - - -
140A GLN 3.5 2.7 + - - -
141A ARG 3.2 0.2 - - - -
142A MET* 1.3 77.7 - - - +
144A GLU* 1.3 61.0 + - - +
146A PHE 3.3 2.9 - - - +
148A CYS* 3.9 7.5 - - - -
171A ALA* 3.6 28.5 - - - -
173A ARG* 3.3 15.7 + - - -
125B HIS* 5.4 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LYS* 2.5 27.6 + - - +
140A GLN* 2.8 35.5 + - - +
141A ARG* 2.7 51.0 + - - +
143A GLY* 1.3 78.8 - - - +
145A LEU* 1.3 58.7 + - + +
106B PHE 4.9 1.2 - - - +
108B PRO* 4.9 3.3 - - - +
124B VAL* 4.7 13.1 - - - +
125B HIS* 6.3 1.6 - - - +
126B GLN* 4.3 34.8 + - + +
128B TYR* 6.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LYS* 3.6 11.3 - - - +
91A ILE 4.9 0.5 + - - -
141A ARG* 3.1 51.4 + - + +
142A MET* 3.3 2.4 + - - +
144A GLU* 1.3 76.7 - - - +
146A PHE* 1.3 83.3 + - + +
238A LEU* 5.1 3.4 - - + -
241A PHE* 4.4 7.2 - - + +
242A GLU* 3.6 42.4 - - + +
245A SER* 3.5 29.8 - - - +
246A ARG* 4.5 0.7 - - - +
108B PRO* 3.9 24.6 - - + +
128B TYR* 4.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LYS* 3.1 22.4 + - - -
91A ILE* 3.4 39.3 - - + +
93A VAL* 3.5 20.2 - - + -
142A MET* 3.0 37.5 + - + +
143A GLY* 3.3 10.2 - - - +
144A GLU 3.3 0.6 - - - -
145A LEU* 1.3 93.5 - - + +
147A GLU* 1.3 60.0 + - - +
148A CYS* 3.5 5.9 + - - -
173A ARG* 4.1 3.1 + - - -
203A LEU* 4.0 10.3 - - + -
241A PHE* 3.6 52.5 - + + -
244A LEU 4.3 0.4 - - - -
245A SER* 3.5 23.1 - - - -
----------------------------------------------------------
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