Contacts of the helix formed by residues 132 - 146 (chain A) in PDB entry 1R4N
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 PRO 132 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLN 4.3 3.1 - - - +
131A LEU* 1.3 92.2 - - + +
133A GLU* 1.3 70.9 + - - +
134A SER* 4.2 11.4 - - - +
135A THR* 3.1 18.3 + - - +
136A SER* 2.9 16.1 + - - -
433A ASP* 4.5 3.1 - - - +
436A HIS* 4.5 18.2 - - + +
442A TYR* 4.1 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU 4.0 0.6 + - - -
132A PRO* 1.3 69.2 - - - +
134A SER* 1.3 68.7 + - - +
136A SER* 2.7 21.0 + - - -
137A LEU* 3.0 24.3 + - + +
402A TYR* 3.5 23.5 + - + +
430A ARG* 2.7 33.4 + - - +
433A ASP* 3.6 45.1 + - + +
434A ARG* 4.8 2.8 + - - +
436A HIS* 6.0 0.4 + - - -
437A LYS* 5.9 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLU* 3.9 7.6 + - - -
132A PRO* 3.4 10.6 - - - +
133A GLU* 1.3 77.4 - - - +
135A THR* 1.3 74.1 + - - -
137A LEU* 3.8 5.4 + - - +
138A ARG* 3.2 23.3 + - - +
437A LYS* 5.9 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PRO* 4.3 15.9 - - + -
110A GLU* 2.4 42.5 + - + +
113A LEU* 4.6 9.0 - - + -
131A LEU* 4.2 21.5 - - + -
132A PRO* 3.1 22.5 + - - +
133A GLU 2.8 2.8 + - - -
134A SER* 1.3 82.2 + - - +
136A SER* 1.3 66.2 + - - +
138A ARG* 3.3 3.1 + - - +
139A LEU* 2.8 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 3.4 35.0 + - - +
132A PRO 2.9 8.2 + - - -
133A GLU* 2.7 17.5 + - - -
135A THR* 1.3 72.4 - - - +
137A LEU* 1.3 59.3 - - - -
139A LEU* 3.7 1.1 - - - +
140A ALA* 2.8 32.2 + - - +
152A ILE* 4.0 25.0 - - - +
398A LEU* 4.0 8.1 - - - -
402A TYR* 6.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU* 3.0 23.9 + - - +
134A SER* 4.2 3.8 - - - +
136A SER* 1.3 81.8 - - - +
138A ARG* 1.3 65.0 + - - +
140A ALA* 3.4 1.6 + - - +
141A ASP* 3.3 22.3 + - - +
398A LEU* 3.8 27.5 - - + +
399A ALA* 4.9 4.3 - - - +
402A TYR* 3.5 51.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLU* 2.9 28.2 + - - -
113A LEU* 2.7 49.7 + - + +
114A ASP* 2.9 33.3 + - - +
134A SER 3.2 17.6 + - - +
135A THR* 3.7 4.0 - - - +
137A LEU* 1.3 80.5 - - - +
139A LEU* 1.3 60.8 + - - +
141A ASP* 3.5 5.0 - - - +
142A VAL* 3.2 27.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
36A ILE* 4.5 11.0 - - + -
109A PRO* 6.0 2.7 - - + -
113A LEU* 3.6 33.6 - - + +
120A PHE* 4.1 17.7 - - + -
126A VAL* 4.7 0.7 - - + -
128A ALA* 4.0 17.3 - - + -
131A LEU* 4.2 10.1 - - + -
135A THR* 2.8 23.5 + - + +
136A SER* 3.7 2.2 - - - +
138A ARG* 1.3 70.5 - - - +
140A ALA* 1.3 55.0 + - - +
141A ASP 2.6 15.6 + - - -
142A VAL* 3.1 1.9 + - + +
143A LEU* 2.9 47.0 + - + +
150A LEU* 3.7 26.5 - - + -
152A ILE* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A SER 2.8 12.8 + - - +
137A LEU 3.9 2.9 - - - +
139A LEU* 1.3 72.4 - - - +
141A ASP* 1.3 54.8 + - - +
143A LEU* 4.8 0.2 - - - +
144A TRP* 3.1 24.2 + - - +
150A LEU* 3.3 27.1 - - + +
165A ILE* 3.7 10.8 - - + +
397A SER* 5.8 0.3 - - - -
398A LEU* 3.2 48.9 + - + +
399A ALA 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU 3.3 16.0 + - - +
138A ARG* 3.5 7.2 - - - +
139A LEU 2.6 1.4 + - - -
140A ALA* 1.3 77.4 - - - +
142A VAL* 1.3 73.6 + - - +
143A LEU 3.0 0.7 - - - -
144A TRP* 2.7 17.2 + - - +
145A ASN* 2.9 32.3 + - - -
399A ALA* 5.2 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.8 27.6 - - + +
117A PRO* 3.7 36.3 - - + +
120A PHE* 5.3 3.4 - - + -
138A ARG* 3.2 21.1 - - + +
139A LEU 3.1 4.2 + - - +
141A ASP* 1.3 83.2 + - - +
143A LEU* 1.3 59.7 + - + +
145A ASN* 3.4 6.2 + - - +
146A SER* 3.0 40.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
120A PHE* 3.4 35.0 - - + -
126A VAL* 3.9 11.4 - - + -
139A LEU* 2.9 37.8 + - + +
140A ALA 4.7 1.6 - - - -
142A VAL* 1.3 75.8 - - + +
144A TRP* 1.3 66.6 + - - +
146A SER* 3.2 3.9 + - - -
147A GLN 3.0 5.0 + - - -
148A ILE* 2.9 60.2 + - + +
150A LEU* 3.2 43.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ALA 3.1 22.0 + - - +
141A ASP* 2.7 15.0 + - - +
143A LEU* 1.3 75.0 - - - +
145A ASN* 1.3 75.5 + - - +
147A GLN* 3.0 22.5 + - - +
148A ILE 4.7 4.3 - - - +
165A ILE* 3.6 22.4 - - + -
166A ILE 4.7 0.2 - - - -
167A LYS* 3.9 54.0 - - + +
395A CYS 3.6 16.2 - - - -
397A SER* 3.2 51.1 - - - -
400A GLU* 5.1 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ASP* 2.9 37.2 + - - -
142A VAL* 3.8 7.7 - - - +
144A TRP* 1.3 87.4 - - - +
146A SER* 1.3 60.1 + - - +
147A GLN* 3.1 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PRO 5.3 2.4 + - - -
118A SER* 5.6 1.9 - - - -
120A PHE* 5.9 1.1 - - - -
121A CYS* 3.8 30.0 - - - -
142A VAL* 3.0 26.3 + - - +
143A LEU* 3.2 6.7 + - - -
145A ASN* 1.3 75.1 - - - +
147A GLN* 1.3 72.1 + - - +
148A ILE* 3.3 16.5 + - - +
----------------------------------------------------------
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