Contacts of the helix formed by residues 129 - 139 (chain A) in PDB entry 4NAT
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 SER 129 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 4.1 7.9 - - - -
19A HIS* 5.7 2.0 - - - -
92A ARG* 3.4 20.6 - - - +
128A ILE* 1.3 71.7 - - - +
130A SER* 1.3 65.3 + - - +
131A SER* 3.8 6.1 - - - -
132A ILE* 2.9 29.0 + - - +
133A VAL* 3.2 22.5 + - - +
203A ADP 4.9 8.3 - - - -
102C ARG* 3.0 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 3.4 29.5 + - - -
14A PRO* 2.6 25.8 + - - +
16A THR* 3.9 10.3 - - - +
19A HIS* 3.4 16.3 + - - -
129A SER* 1.3 70.5 - - - +
131A SER* 1.3 65.4 + - - +
133A VAL* 3.3 2.6 + - - +
134A LYS* 3.0 31.0 + - - +
203A ADP 4.6 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A SER* 3.2 9.5 - - - -
130A SER* 1.3 80.9 - - - +
132A ILE* 1.3 57.4 + - - +
134A LYS* 3.5 13.9 + - - +
135A GLU* 3.1 26.3 + - - +
102C ARG* 4.1 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 3.2 27.4 - - + +
128A ILE* 3.7 13.7 - - + -
129A SER* 2.9 31.9 + - - +
131A SER* 1.3 71.5 - - - +
133A VAL* 1.3 69.5 + - + +
135A GLU* 3.8 10.2 - - - +
136A VAL* 3.1 26.3 + - - +
102C ARG* 4.2 18.5 - - + +
103C LEU* 5.0 10.1 - - + -
106C MET* 3.4 34.3 - - + -
201C 2W5 4.4 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO* 5.2 3.1 - - + -
16A THR* 4.3 3.4 - - + -
128A ILE* 3.9 15.0 - - + -
129A SER 3.2 17.7 + - - +
130A SER* 3.7 5.6 - - - +
132A ILE* 1.3 80.6 - - + +
134A LYS* 1.3 57.7 + - - +
136A VAL* 3.5 7.7 + - - +
137A ALA* 2.8 31.4 + - - +
143A ILE* 4.5 6.5 - - + +
146A PHE* 3.7 30.5 - - + -
147A VAL* 3.7 16.4 - - + -
155A LEU* 3.3 30.3 - - + -
106C MET* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 2.9 41.5 + - - +
14A PRO* 4.1 11.7 - - + -
45A GLY* 5.4 0.2 - - - -
46A THR* 3.0 33.1 - - + +
130A SER* 3.0 26.5 + - - +
131A SER* 3.8 9.9 - - - +
133A VAL* 1.3 72.7 - - - +
135A GLU* 1.3 65.1 + - - +
137A ALA* 3.7 6.6 - - - +
138A ALA* 3.0 22.7 + - - +
155A LEU* 4.1 11.7 - - + -
159A PHE* 4.0 15.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER 3.1 17.8 + - - +
132A ILE* 3.8 12.3 - - - +
133A VAL 3.3 0.4 - - - -
134A LYS* 1.3 74.6 - - - +
136A VAL* 1.3 64.6 + - - +
138A ALA* 3.2 13.9 + - - +
139A TYR* 3.1 34.4 + - + -
38C LEU* 5.9 1.2 - - - +
103C LEU* 5.8 2.1 - - - +
201C 2W5 3.4 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE 3.1 11.7 + - - +
133A VAL* 3.6 9.2 - - - +
135A GLU* 1.3 79.2 - - - +
137A ALA* 1.3 63.0 + - - +
139A TYR* 3.1 16.9 + - - +
141A ALA* 3.1 29.3 + - + +
143A ILE* 3.7 19.3 - - + -
146A PHE* 4.2 15.3 - - + -
74C LEU* 4.5 2.5 - - + -
106C MET* 3.9 19.1 - - + -
110C LEU* 3.9 16.6 - - + -
201C 2W5 3.7 31.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
133A VAL 2.8 20.0 + - - +
134A LYS* 3.7 7.9 - - - +
136A VAL* 1.3 74.6 - - - +
138A ALA* 1.3 60.4 + - - +
140A ARG* 3.0 20.0 + - - +
141A ALA 4.7 2.7 - - - +
143A ILE* 4.2 18.4 - - + -
155A LEU* 4.3 18.6 - - + +
156A LYS* 6.3 0.2 - - - -
159A PHE* 3.7 27.1 - - + +
160A LYS 4.5 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS 3.0 14.5 + - - +
135A GLU* 3.2 12.3 + - - +
137A ALA* 1.3 75.5 - - - +
139A TYR* 1.3 65.7 + - + +
140A ARG* 3.4 3.9 + - - +
159A PHE* 3.9 34.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
135A GLU* 3.1 44.9 + - + -
136A VAL 3.1 7.8 + - - +
138A ALA* 1.3 82.3 - - + +
140A ARG* 1.3 69.3 + - - +
141A ALA 3.3 2.1 + - - -
38C LEU* 3.4 30.9 - - + +
72C SER 4.8 0.2 - - - -
73C GLY* 3.7 37.7 - - - -
74C LEU* 3.5 36.3 - - + +
77C ASP* 5.4 1.2 - - - +
201C 2W5 3.9 12.9 - - - -
----------------------------------------------------------
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