Contacts of the helix formed by residues 133 - 148 (chain A) in PDB entry 5H4G
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 LEU 133 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 4.2 6.5 - - + -
13A ALA* 4.1 18.2 - - + +
16A LYS* 4.3 15.7 - - + -
17A MET* 4.1 17.9 - - + -
113A VAL* 3.6 23.8 - - + -
114A THR 2.9 20.5 + - - +
115A ASP* 2.8 36.7 - - - +
131A MET 3.4 0.8 + - - -
132A PRO* 1.3 72.9 - - - +
134A ASP* 1.3 58.8 + - - +
136A PHE* 3.1 3.6 + - + +
137A ILE* 2.8 55.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASP* 4.6 5.9 + - - +
132A PRO* 4.2 14.6 - - - -
133A LEU* 1.3 77.5 - - - +
135A LYS* 1.3 61.3 + - - +
137A ILE* 3.4 9.7 + - - +
138A LYS* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A MET* 3.5 22.7 - - + +
132A PRO* 3.1 24.8 + - + +
133A LEU 3.1 0.4 - - - -
134A ASP* 1.3 81.9 - - - +
136A PHE* 1.3 63.9 + - - +
138A LYS* 3.3 7.1 + - + +
139A GLU* 3.0 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 4.1 21.1 - - + -
7A ILE* 3.6 31.0 - - + -
9A PHE* 3.9 22.2 - + - -
17A MET* 4.2 7.0 - - + -
29A THR* 3.7 25.8 - - + -
33A PHE* 4.0 22.4 - + - -
113A VAL* 3.6 27.6 - - + -
131A MET* 3.9 11.6 - - - +
132A PRO 3.1 5.0 + - - +
133A LEU* 3.1 12.5 + - + +
135A LYS* 1.3 75.3 - - - +
137A ILE* 1.3 69.6 + - - +
139A GLU* 3.2 4.7 + - - +
140A VAL* 2.9 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 4.7 7.9 - - + -
17A MET* 4.4 9.2 - - - -
22A MET* 4.0 33.0 - - + -
25A ILE* 4.3 5.1 - - + +
133A LEU* 2.8 51.0 + - + +
134A ASP* 3.8 8.7 - - - +
136A PHE* 1.3 77.6 - - - +
138A LYS* 1.3 53.3 + - - +
140A VAL* 3.2 6.1 + - - +
141A GLU* 2.8 54.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ASP 3.0 17.9 + - - +
135A LYS* 3.5 8.7 - - + +
137A ILE* 1.3 76.6 - - - +
139A GLU* 1.3 64.2 + - + +
141A GLU* 3.3 15.1 + - - +
142A LEU* 3.1 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO 5.7 2.9 - - - -
3A LEU* 4.0 22.4 - - + -
131A MET* 4.2 11.9 - - + -
135A LYS* 3.0 43.0 + - - +
136A PHE* 3.2 6.9 + - - +
138A LYS* 1.3 76.7 - - + +
140A VAL* 1.3 61.1 + - - +
142A LEU* 3.2 21.1 + - - +
143A MET* 3.2 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 3.6 39.7 - - + +
28A VAL* 3.7 23.1 - - + -
29A THR* 3.8 8.3 - - - +
33A PHE* 4.9 2.9 - - + -
136A PHE* 2.9 49.6 + - + +
137A ILE 3.8 5.2 - - - +
139A GLU* 1.3 70.5 - - + +
141A GLU* 1.3 67.4 + - - +
143A MET* 3.1 20.2 + - + +
144A VAL* 3.0 20.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
22A MET* 5.9 0.3 - - - +
25A ILE* 3.5 21.6 - - + +
137A ILE* 2.8 34.7 + - + +
138A LYS* 3.5 14.0 - - - +
140A VAL* 1.3 71.8 - - - +
142A LEU* 1.3 63.0 + - + +
144A VAL* 3.2 6.6 + - - +
145A GLU* 3.1 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LYS* 3.1 21.6 + - + +
139A GLU* 3.6 23.3 - - - +
140A VAL 3.1 0.6 - - - -
141A GLU* 1.3 72.6 - - + +
143A MET* 1.3 66.8 + - + +
145A GLU* 3.3 23.8 + - + +
146A LYS* 2.9 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 4.2 24.9 - - + -
28A VAL* 4.0 20.9 - - + -
32A LYS* 3.7 37.0 - - + +
33A PHE* 4.3 15.9 - - + -
139A GLU* 3.2 17.2 + - + +
140A VAL* 3.1 16.0 + - + +
142A LEU* 1.3 77.4 - - - +
144A VAL* 1.3 56.6 + - - +
146A LYS* 3.4 7.7 + - - +
147A GLU* 3.0 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 4.5 22.2 - - + +
25A ILE* 4.3 12.8 - - + -
28A VAL* 4.1 22.0 - - + -
140A VAL* 3.0 18.9 + - + +
141A GLU* 3.4 11.4 - - - +
142A LEU 3.2 0.2 - - - -
143A MET* 1.3 75.3 - - - +
145A GLU* 1.3 66.5 + - - +
146A LYS 3.4 0.2 + - - -
147A GLU* 3.5 22.6 + - - +
148A LEU* 3.5 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLU 3.1 10.0 + - - +
142A LEU* 3.5 30.6 - - + +
144A VAL* 1.3 80.3 - - - +
146A LYS* 1.3 56.0 + - - +
148A LEU* 3.0 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU 2.9 18.6 + - - +
143A MET* 3.6 9.0 - - - +
145A GLU* 1.3 70.4 - - - +
147A GLU* 1.3 66.5 + - - +
148A LEU* 3.0 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 4.0 32.1 - - - +
32A LYS* 5.1 9.4 + - - +
143A MET 3.0 19.9 + - - +
144A VAL* 3.6 14.7 - - - +
145A GLU 3.4 0.2 - - - -
146A LYS* 1.3 74.7 - - - +
148A LEU* 1.3 68.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A VAL 3.5 4.8 + - - -
145A GLU* 3.0 22.6 + - - +
146A LYS* 3.4 14.4 - - - +
147A GLU* 1.3 83.5 - - - +
----------------------------------------------------------
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