Contacts of the helix formed by residues 132 - 152 (chain A) in PDB entry 4JCQ
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 GLU 132 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ILE* 1.3 84.0 + - - +
133A ALA* 1.3 65.8 + - - +
134A LYS* 3.3 27.8 - - + +
135A GLU* 3.1 7.5 + - + +
136A ILE* 3.1 19.3 + - - +
165B ASN* 4.9 16.8 - - + +
167B TRP* 6.1 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU* 1.3 75.0 + - - +
134A LYS* 1.3 63.6 + - - +
136A ILE* 3.2 15.1 + - + +
137A ILE* 3.0 30.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
132A GLU* 4.3 20.9 - - + +
133A ALA* 1.3 78.6 - - - +
135A GLU* 1.3 65.8 + - + +
137A ILE* 3.6 7.2 + - - +
138A ARG* 3.1 33.4 + - - +
165B ASN 6.0 2.0 - - - -
166B PHE* 5.9 8.7 - - + -
----------------------------------------------------------
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 ILE* 3.8 10.5 - - + -
132A GLU* 3.1 14.8 + - + +
134A LYS* 1.3 85.7 - - + +
136A ILE* 1.3 58.3 + - - +
137A ILE 3.3 0.4 - - - -
138A ARG* 3.4 24.5 + - - +
139A MET* 2.9 33.8 + - + +
112B ARG* 3.2 45.0 + - - +
167B TRP* 3.4 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ALA* 3.4 44.8 - - + +
120A GLY* 4.8 4.5 - - - -
131A ILE* 3.7 22.2 - - + +
132A GLU 3.1 15.0 + - - +
133A ALA* 3.2 16.6 + - + +
135A GLU* 1.3 75.9 - - - +
137A ILE* 1.3 63.5 + - + +
139A MET* 3.5 5.4 + - - +
140A ARG* 3.0 31.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
133A ALA* 3.0 17.3 + - + +
134A LYS* 3.7 9.9 - - - +
135A GLU 3.3 0.2 - - - -
136A ILE* 1.3 80.3 - - + +
138A ARG* 1.3 61.3 + - + +
140A ARG* 3.3 8.1 + - + +
141A GLU* 2.9 52.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
134A LYS* 3.1 22.7 + - - +
135A GLU* 3.4 23.5 + - - +
137A ILE* 1.3 76.1 - - + +
139A MET* 1.3 62.4 + - - +
141A GLU* 3.4 11.8 + - - +
142A ARG* 3.0 24.3 + - - +
167B TRP 3.5 16.8 + - - -
169B SER* 3.9 15.4 + - - +
172B GLU* 2.7 45.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 3.9 26.0 - - + -
118A PRO 4.8 3.1 - - - +
119A ALA 4.3 12.3 - - - +
120A GLY 4.1 10.1 - - - +
121A GLY* 4.1 13.7 - - - -
131A ILE* 5.3 6.5 - - + -
135A GLU* 2.9 21.6 + - - +
136A ILE* 3.7 5.2 - - - +
138A ARG* 1.3 76.1 - - - +
140A ARG* 1.3 62.9 + - - +
142A ARG* 3.3 20.4 + - - +
143A ILE* 3.0 44.6 + - + +
112B ARG* 3.4 39.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLN* 2.7 39.9 + - - +
118A PRO 3.9 1.4 + - - -
119A ALA* 3.7 24.7 - - - +
136A ILE* 3.0 22.1 + - + +
137A ILE* 3.6 8.7 - - + +
139A MET* 1.3 77.6 - - - +
141A GLU* 1.3 56.9 + - + +
143A ILE* 3.4 5.4 + - - +
144A ASN* 2.8 61.3 + - - +
159A SER* 4.8 1.9 + - - +
162A THR* 3.6 10.1 + - - -
163A ASP* 2.9 48.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
137A ILE* 2.9 40.4 + - + +
138A ARG* 3.7 11.1 - - - +
140A ARG* 1.3 75.9 - - + +
142A ARG* 1.3 62.4 + - - +
144A ASN* 3.5 1.4 + - - +
145A ARG* 3.0 55.5 + - - +
155A TYR* 3.3 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 3.8 15.4 - - - +
68A ASP* 2.8 40.7 + - - -
138A ARG 3.0 16.4 + - - +
139A MET* 3.3 16.4 + - - +
141A GLU* 1.3 76.7 - - - +
143A ILE* 1.3 75.5 + - - +
145A ARG* 3.8 8.8 - - - +
146A LEU* 3.1 24.4 + - - +
109B PRO 5.3 2.2 - - - -
110B ASN* 2.8 51.8 + - - +
111B THR 5.5 1.5 - - - +
112B ARG* 5.9 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 3.9 19.7 - - + -
68A ASP* 5.2 2.0 - - - +
95A THR* 4.2 14.8 - - + +
117A GLN* 3.8 34.1 - - + +
118A PRO 6.1 0.4 - - - +
139A MET* 3.0 37.8 + - + +
140A ARG* 4.0 6.3 - - - +
142A ARG* 1.3 87.3 - - - +
144A ASN* 1.3 66.5 + - - +
146A LEU* 3.3 8.2 + - + +
147A ILE* 3.0 44.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 2.8 46.2 + - - +
141A GLU 3.7 0.2 - - - +
142A ARG 3.4 0.2 - - - -
143A ILE* 1.3 73.3 - - - +
145A ARG* 1.3 56.6 + - - +
148A ALA* 2.9 30.0 + - - +
155A TYR* 3.5 29.1 + - + -
158A ILE* 3.5 13.0 - - + +
159A SER* 3.5 34.2 + - - +
162A THR* 2.7 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLU* 3.0 54.1 + - - +
142A ARG* 3.8 8.0 - - - +
143A ILE 3.3 0.2 - - - -
144A ASN* 1.3 72.7 - - - +
146A LEU* 1.3 66.0 + - - +
148A ALA* 3.8 5.6 - - - +
149A GLU* 3.0 27.3 + - - +
155A TYR* 3.7 24.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 5.3 0.2 - - - +
71A HIS* 3.7 41.7 - - + +
95A THR* 4.0 28.3 - - + +
98A LEU* 4.7 10.8 - - + +
142A ARG* 3.1 18.4 + - - +
143A ILE* 3.4 11.9 - - + +
145A ARG* 1.3 76.8 - - - +
147A ILE* 1.3 70.8 + - + +
149A GLU* 3.5 5.3 + - - +
150A ALA* 3.2 25.1 + - + +
110B ASN* 3.9 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ILE* 4.4 9.0 - - + -
95A THR* 4.9 2.2 - - - +
98A LEU* 3.8 28.0 - - + -
115A ILE* 4.4 13.9 - - + +
117A GLN* 3.7 26.2 - - - +
143A ILE* 3.0 31.5 + - + +
146A LEU* 1.3 79.7 - - + +
148A ALA* 1.3 55.7 + - - +
150A ALA 3.4 0.3 + - - -
151A THR* 2.7 44.0 + - + +
158A ILE* 3.7 28.5 - - + -
162A THR* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASN 2.9 18.8 + - - +
145A ARG* 3.8 8.3 - - - +
146A LEU 3.4 0.2 - - - -
147A ILE* 1.3 76.3 - - - +
149A GLU* 1.3 56.7 - - - +
151A THR* 3.9 0.7 - - - -
152A GLY* 2.9 26.9 + - - -
153A GLN 3.2 24.4 - - - +
154A SER 4.2 4.7 - - - +
155A TYR* 4.2 13.0 - - + +
158A ILE* 3.7 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LYS* 5.3 6.9 + - - -
145A ARG 3.0 18.3 + - - +
146A LEU* 3.9 5.4 - - - +
148A ALA* 1.3 77.8 - - - +
150A ALA* 1.3 62.5 + - - +
152A GLY* 4.0 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.8 42.6 - - + +
102A LYS* 4.4 7.4 - - - +
105A ARG* 2.8 27.7 + - - +
146A LEU* 3.2 18.5 + - + +
147A ILE 3.9 2.9 - - - +
149A GLU* 1.3 79.0 - - - +
151A THR* 1.3 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.0 10.5 - - + -
102A LYS* 4.1 9.2 - - - -
147A ILE* 2.7 37.6 + - + +
148A ALA 3.6 0.3 + - - -
150A ALA* 1.3 78.3 - - - +
152A GLY* 1.3 60.5 + - - +
153A GLN* 3.2 22.3 + - - +
158A ILE* 3.9 1.9 - - - +
176A TYR* 3.9 18.3 - - + +
177A GLY* 3.5 30.3 - - - +
178A ILE* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ALA 2.9 10.0 + - - -
149A GLU 4.0 5.2 + - - -
150A ALA 3.6 1.8 - - - -
151A THR* 1.3 77.6 - - - +
153A GLN* 1.3 63.9 + - - +
154A SER 4.0 0.2 + - - -
----------------------------------------------------------
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