Contacts of the helix formed by residues 133 - 146 (chain A) in PDB entry 5LTU
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 LYS 133 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLN* 3.9 21.2 + - - +
46A TRP 4.3 10.5 - - - +
47A ILE* 4.0 21.4 - - + +
89A ARG* 4.5 24.7 - - - +
129A LEU* 2.7 20.6 + - + +
132A HIS* 1.3 78.4 + - - +
134A PRO* 1.3 62.9 - - + +
135A VAL* 3.2 12.3 - - + -
136A HIS* 2.9 47.0 + - + +
137A ALA 3.3 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU 3.2 7.2 - - - +
130A GLN* 4.2 18.8 - - + +
131A CYS 4.9 2.5 - - - +
132A HIS* 3.8 5.4 - - - +
133A LYS* 1.3 88.5 - - + +
135A VAL* 1.3 68.5 + - + +
136A HIS 3.2 0.2 - - - -
137A ALA* 3.3 17.5 + - + +
138A GLU* 3.3 16.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
20A ARG* 6.2 0.4 - - - +
86A ASN* 4.2 24.5 - - - +
89A ARG* 5.3 11.2 - - - +
133A LYS* 3.1 12.7 + - + -
134A PRO* 1.3 83.6 - - + +
136A HIS* 1.3 82.9 + - + +
138A GLU* 3.5 22.0 + - - +
139A TYR* 3.5 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 4.7 10.3 + - - -
47A ILE* 3.7 20.3 - - + +
48A VAL* 3.1 47.8 + - + +
89A ARG* 5.8 2.4 + - - -
129A LEU* 4.1 19.5 - - + +
133A LYS* 2.9 26.5 + - + +
135A VAL* 1.3 97.1 - - + +
137A ALA* 1.3 64.7 + - - +
138A GLU 3.2 0.7 - - - -
139A TYR* 3.1 46.5 + + - +
140A LEU* 3.7 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ILE* 4.1 6.5 - - - +
129A LEU* 3.9 24.5 - - + +
130A GLN* 3.7 32.1 - - + +
133A LYS 3.3 2.8 + - - -
134A PRO 3.3 13.4 + - - +
136A HIS* 1.3 79.2 - - - +
138A GLU* 1.3 55.8 + - - +
140A LEU* 3.2 6.9 + - - +
141A GLU* 2.9 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 4.0 17.6 - - + -
134A PRO 3.3 13.3 + - - +
135A VAL* 3.6 15.2 - - - +
136A HIS 3.2 0.6 - - - -
137A ALA* 1.3 74.7 - - - +
139A TYR* 1.3 66.5 + - - +
141A GLU* 3.7 19.6 - - - +
142A LYS* 3.0 26.9 + - - +
202A EDO 3.7 35.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 3.8 20.0 + - - -
22A ALA* 4.3 13.0 - - + -
24A LEU* 4.2 18.2 - - + -
48A VAL* 4.4 17.7 - - + -
81A LEU* 3.3 14.4 - - - +
84A PHE* 3.8 41.4 - + + +
93A THR* 3.9 10.3 + - + +
95A VAL* 3.8 29.2 - - + -
135A VAL* 3.5 20.8 - - + +
136A HIS* 3.1 38.6 + + + +
138A GLU* 1.3 78.4 - - - +
140A LEU* 1.3 60.5 + - - +
142A LYS* 3.7 0.5 + - - +
143A LEU* 3.3 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.7 33.0 - - + -
26A PHE* 4.6 1.8 - - + -
34A VAL* 4.2 22.4 - - + -
36A LEU* 5.1 2.0 - - + -
48A VAL* 5.1 0.4 - - + -
122A VAL* 4.5 9.0 - - + +
125A ALA* 3.8 25.1 - - + -
126A ILE* 3.7 18.2 - - + +
129A LEU* 3.6 29.6 - - + -
136A HIS 3.7 2.0 + - - +
137A ALA 3.2 5.4 + - - +
139A TYR* 1.3 78.8 - - - +
141A GLU* 1.3 65.3 + - - +
143A LEU* 3.3 19.4 + - + +
144A LYS* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ILE* 4.2 11.2 - - + -
130A GLN* 2.7 34.7 + - - +
137A ALA* 2.9 22.6 + - - +
138A GLU* 3.3 21.9 + - - +
140A LEU* 1.3 76.1 - - - +
142A LYS* 1.3 57.3 + - - +
144A LYS 3.1 2.6 + - - -
145A LEU* 3.0 37.9 + - + +
145B LEU* 3.6 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 4.6 9.7 - - + +
84A PHE* 4.1 19.5 - - + -
138A GLU 3.0 16.4 + - - +
139A TYR 4.0 4.0 - - - +
141A GLU* 1.3 74.3 - - - +
143A LEU* 1.3 65.3 + - - +
145A LEU* 4.0 9.0 - - - +
146A GLY* 3.2 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 4.6 2.5 - - + -
26A PHE* 3.7 26.0 - - + -
31A GLU* 4.0 11.0 - - - +
79A ARG* 3.4 30.3 + - - +
81A LEU* 4.0 19.4 - - + +
97A VAL* 4.0 20.2 - - + -
122A VAL* 5.0 0.7 - - + -
139A TYR 3.3 11.9 + - - +
140A LEU* 3.3 21.7 + - + +
141A GLU 3.2 0.2 - - - -
142A LYS* 1.3 80.1 - - - +
144A LYS* 1.3 83.3 + - + +
146A GLY* 3.3 16.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLN 5.2 0.6 + - - -
31A GLU* 3.3 21.9 + - - +
32A ASP* 4.0 11.7 + - - -
122A VAL* 3.5 39.7 - - + +
126A ILE* 4.7 4.0 - - + -
140A LEU 3.1 13.4 + - - +
141A GLU 3.1 5.4 + - - +
143A LEU* 1.3 86.1 - - + +
145A LEU* 1.3 65.7 + - - +
146A GLY 3.1 5.1 + - - -
144B LYS* 3.6 37.0 - - - +
145B LEU* 3.9 13.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
141A GLU* 3.0 26.4 + - + +
142A LYS* 3.6 7.8 + - - +
144A LYS* 1.3 76.0 - - - +
146A GLY* 1.3 59.7 + - - +
122B VAL* 4.3 9.5 - - + +
123B GLU* 3.9 33.9 + - + +
126B ILE* 4.0 30.3 - - + -
141B GLU* 4.8 4.9 - - + -
144B LYS* 3.7 28.1 - - + -
145B LEU* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS 3.2 13.2 + - - -
143A LEU 3.3 12.1 + - - -
144A LYS 3.1 4.9 - - - -
145A LEU* 1.3 83.4 - - - +
32B ASP* 4.9 11.5 - - - +
123B GLU* 5.4 4.0 - - - -
----------------------------------------------------------
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