Contacts of the helix formed by residues 129 - 142 (chain A) in PDB entry 5NUJ
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 ASP 129 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.3 4.3 - - - +
101A LYS* 4.4 25.3 - - - +
102A TYR* 5.3 2.9 - - - +
123A VAL* 4.5 12.8 - - + -
127A GLU* 3.2 10.7 + - + +
128A VAL* 1.3 69.4 - - - +
130A ASP* 1.3 60.8 + - - +
131A GLU* 2.8 36.2 + - - +
132A ALA* 2.8 31.9 + - + +
133A LEU* 3.2 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 3.1 25.9 + - - +
129A ASP* 1.3 71.3 + - - +
131A GLU* 1.3 62.3 + - - +
133A LEU* 3.3 19.7 + - - +
134A GLU* 3.4 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ASP* 2.8 11.7 + - - +
130A ASP* 1.3 80.4 - - - +
132A ALA* 1.3 61.6 + - - +
134A GLU* 3.2 37.0 + - - +
135A LYS* 3.5 23.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
102A TYR* 3.9 27.8 - - + -
104A LEU* 4.6 2.3 - - - +
121A CYS* 3.8 22.9 - - - -
123A VAL* 4.5 3.1 - - + -
129A ASP* 2.8 34.0 + - + +
131A GLU* 1.3 73.0 - - - +
133A LEU* 1.3 61.0 + - + +
135A LYS* 3.5 8.7 + - - +
136A PHE* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.4 31.4 - - + -
23A ALA* 4.3 13.9 - - + -
121A CYS* 4.3 10.1 - - + -
128A VAL* 3.8 28.5 - - + -
129A ASP 3.2 11.0 + - - +
130A ASP* 3.7 13.7 - - - +
131A GLU 3.2 1.0 - - - -
132A ALA* 1.3 73.7 - - - +
134A GLU* 1.3 59.6 + - - +
136A PHE* 3.4 7.5 + - + +
137A ASP* 2.8 40.2 + - - +
148A ARG* 5.2 17.3 - - - +
150A SER* 5.3 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ASP* 3.4 15.8 + - - +
131A GLU* 3.2 26.1 + - - +
133A LEU* 1.3 73.0 - - - +
135A LYS* 1.3 58.9 + - + +
137A ASP* 2.8 12.5 + - - +
138A LYS* 2.7 60.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
96A ASP* 4.3 7.9 - - - +
98A ASP* 5.6 1.0 - - - +
102A TYR* 2.9 47.0 + - + +
104A LEU* 4.2 14.1 - - + +
131A GLU* 3.5 24.9 + - + +
132A ALA* 3.5 9.5 + - - +
133A LEU 3.4 0.4 - - - -
134A GLU* 1.3 81.2 - - + +
136A PHE* 1.3 62.0 + - - +
138A LYS* 3.3 12.2 + - + +
139A ALA* 3.0 24.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
23A ALA* 4.1 22.4 - - + -
25A ALA* 4.5 4.9 - - + -
95A LEU* 6.1 0.9 - - + -
104A LEU* 4.0 18.3 - - + +
105A PHE 5.7 0.2 - - - -
119A CYS* 4.1 13.5 - - + -
120A GLN* 3.3 36.6 - - - -
121A CYS* 3.8 29.4 - - + -
132A ALA 3.2 11.5 + - - +
133A LEU* 3.4 11.2 - - + +
134A GLU 3.1 0.2 - - - -
135A LYS* 1.3 79.7 - - - +
137A ASP* 1.3 71.4 + - - +
139A ALA* 3.3 2.6 + - + +
140A LEU* 3.2 56.8 + - + +
148A ARG* 4.4 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LEU* 2.8 22.4 + - - +
134A GLU* 2.8 11.6 + - - +
136A PHE* 1.3 79.1 - - - +
138A LYS* 1.3 67.4 + - - +
140A LEU* 3.2 14.6 + - - +
141A LYS* 3.3 14.3 + - - +
148A ARG* 2.7 34.3 + - - -
----------------------------------------------------------
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 GLU* 2.7 53.3 + - - +
135A LYS* 3.6 12.5 - - + +
137A ASP* 1.3 73.2 - - - +
139A ALA* 1.3 63.9 + - - +
140A LEU 3.1 1.6 + - - -
141A LYS* 3.3 37.8 + - + +
142A ALA* 4.2 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN* 4.0 28.1 - - - +
95A LEU* 3.9 26.4 - - + +
104A LEU* 4.6 3.6 - - + -
135A LYS 3.0 16.3 + - - +
136A PHE* 3.6 7.9 - - - +
137A ASP 3.3 0.2 - - - -
138A LYS* 1.3 75.7 - - - +
140A LEU* 1.3 63.7 + - + +
142A ALA* 3.9 11.8 - - - +
143A LEU* 3.6 14.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
25A ALA* 3.8 20.2 - - + -
95A LEU* 5.0 4.0 - - + -
119A CYS* 4.5 10.3 - - + -
136A PHE* 3.2 57.8 + - + +
137A ASP* 3.2 7.9 + - - +
138A LYS 3.1 1.2 - - - -
139A ALA* 1.3 85.2 - - + +
141A LYS* 1.3 52.6 + - - +
142A ALA 3.0 6.1 - - - -
143A LEU* 2.4 48.0 + - + +
145A MET* 4.1 23.7 - - + +
148A ARG* 5.4 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ASP 3.3 12.5 + - - +
138A LYS* 3.3 31.7 + - + +
140A LEU* 1.3 74.6 - - - +
142A ALA* 1.3 59.7 + - - +
143A LEU 3.1 4.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR* 5.0 9.2 - - - +
138A LYS 4.2 1.9 + - - +
139A ALA* 3.9 14.7 + - - +
140A LEU 2.9 0.6 + - - -
141A LYS* 1.3 82.0 - - - +
143A LEU* 1.3 67.6 + - + +
144A PRO* 4.5 1.9 - - - +
----------------------------------------------------------
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