Contacts of the helix formed by residues 127 - 145 (chain A) in PDB entry 4R54
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 ASN 127 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 3.2 17.4 - - - +
126A PRO* 1.3 73.6 - - - +
128A CYS* 1.3 60.5 + - - +
129A SER* 3.0 23.8 + - - -
130A THR* 3.0 11.7 + - - +
131A ILE* 2.9 25.2 + - - +
220A GLU* 2.8 41.4 + - - +
223A LYS* 4.6 5.8 - - + -
224A MET* 4.5 1.9 - - - +
227A GLU* 2.9 21.5 + - - +
403A NAP 3.5 7.4 + - - -
404A ACT 3.3 18.4 - - - +
405A 3JM 3.6 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASN* 1.3 69.3 - - - +
129A SER* 1.3 66.0 + - - +
131A ILE* 3.1 13.3 + - - +
132A GLN* 3.2 18.6 + - - +
159A GLY* 5.5 0.2 - - - -
252A HIS* 3.2 35.0 - - + -
325A ASN* 3.8 11.7 - - + +
329A GLY* 3.3 32.6 - - - +
403A NAP 2.6 28.3 + - - +
404A ACT 3.3 23.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASN* 3.0 11.3 + - - -
128A CYS* 1.3 77.5 - - - +
130A THR* 1.3 63.7 + - - +
132A GLN* 3.6 2.8 - - - +
133A MET* 3.4 14.6 + - - +
153A THR* 4.6 0.4 - - - -
155A GLN* 3.1 36.0 + - - +
220A GLU* 3.4 4.6 + - - -
224A MET* 3.8 19.6 - - - +
252A HIS* 3.5 8.9 - - - -
254A GLU* 2.6 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PRO* 4.5 1.8 - - + -
127A ASN* 3.0 13.4 + - - +
129A SER* 1.3 77.6 - - - +
131A ILE* 1.3 65.8 + - - +
133A MET* 3.2 7.7 + - - +
134A MET* 2.9 32.5 + - + +
224A MET* 3.5 26.9 - - - +
227A GLU* 3.2 28.9 + - + +
228A THR* 4.1 15.3 - - - +
231A ILE* 3.7 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A VAL* 4.1 13.0 - - + +
125A CYS* 3.8 15.5 - - - -
126A PRO* 3.2 40.4 - - + +
127A ASN 2.9 13.6 + - - +
128A CYS* 3.1 6.4 + - - +
130A THR* 1.3 77.4 - - - +
132A GLN* 1.3 63.7 + - - +
134A MET* 3.1 3.6 + - - +
135A VAL* 3.1 20.4 + - - +
328A LYS* 3.5 54.7 - - + +
329A GLY* 3.5 15.0 - - - +
333A ASN* 3.9 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A CYS 3.2 10.4 + - - +
129A SER* 3.6 7.4 - - - +
131A ILE* 1.3 81.0 - - - +
133A MET* 1.3 64.4 + - - +
135A VAL* 3.3 1.7 + - - +
136A ALA 3.2 17.3 + - - -
252A HIS* 3.2 34.7 + - - +
254A GLU* 3.4 26.7 + - - +
302A THR* 3.6 22.5 - - + +
321A VAL* 3.1 35.2 + - + +
323A SER* 3.5 35.4 - - - +
325A ASN* 5.3 2.3 - - - -
328A LYS* 5.4 1.1 - - + -
329A GLY* 5.9 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A SER 3.4 4.4 + - - +
130A THR* 3.2 9.4 + - - +
132A GLN* 1.3 81.2 - - - +
134A MET* 1.3 66.9 + - + +
136A ALA* 3.3 6.2 + - - +
137A LEU* 2.9 50.7 + - + +
149A ILE* 3.9 31.2 - - + -
151A VAL* 4.0 17.0 - - + -
224A MET* 3.9 27.4 - - + +
228A THR* 3.5 24.5 - - - +
239A VAL* 4.8 4.7 - - + -
254A GLU* 3.5 14.4 - - - +
256A VAL* 4.4 9.2 - - + -
321A VAL* 4.7 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A VAL* 4.4 11.7 - - + -
111A VAL* 4.0 9.4 - - + +
130A THR* 2.9 27.6 + - + +
131A ILE* 3.1 8.9 + - - +
133A MET* 1.3 96.2 - - + +
135A VAL* 1.3 56.7 + - - +
137A LEU* 4.9 0.7 - - + -
138A GLU* 2.9 36.4 + - - +
149A ILE* 4.7 3.6 - - + -
228A THR* 3.4 42.4 - - + +
231A ILE* 3.9 21.3 - - + -
232A MET* 3.7 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A VAL* 3.9 12.6 - - + -
110A GLU* 4.4 5.4 - - - +
111A VAL* 4.8 2.2 - - + -
131A ILE* 3.1 13.7 + - + +
132A GLN 3.7 7.0 - - - +
133A MET 3.3 0.4 - - - -
134A MET* 1.3 76.4 - - - +
136A ALA* 1.3 61.9 + - - +
139A PRO* 3.3 17.3 - - - +
276A PHE* 3.4 18.9 - - + -
277A PRO 4.4 0.2 - - - +
278A GLY* 3.7 33.2 - - - +
279A ALA* 3.8 11.7 - - + +
302A THR* 4.0 13.2 - - - +
328A LYS* 3.7 28.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLN 3.2 12.0 + - - +
133A MET* 3.3 7.4 + - - +
135A VAL* 1.3 76.9 - - - +
137A LEU* 1.3 60.4 + - + +
139A PRO* 3.4 16.8 - - - +
140A VAL* 4.1 3.1 - - - +
273A ILE* 3.6 15.9 - - - +
279A ALA* 5.1 2.2 - - - -
302A THR* 4.8 0.6 - - + +
304A VAL* 3.7 30.1 - - + -
319A MET* 4.4 8.3 - - - -
321A VAL* 3.8 22.2 - - + -
----------------------------------------------------------
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 MET* 2.9 36.8 + - + +
134A MET* 4.9 1.6 - - + -
136A ALA* 1.3 76.4 - - + +
138A GLU* 1.3 66.1 + - - +
139A PRO 3.3 2.9 - - - -
140A VAL* 2.9 9.0 + - + +
141A ARG* 2.9 22.3 + - - +
146A LEU* 4.2 6.6 - - + +
149A ILE* 3.5 31.6 - - + -
232A MET* 4.0 13.5 - - + -
256A VAL* 4.1 6.3 - - + -
258A ILE* 3.8 33.7 - - + -
319A MET* 3.8 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A VAL* 3.9 37.5 - - + +
134A MET 2.9 19.6 + - - +
137A LEU* 1.3 77.3 - - - +
139A PRO* 1.3 67.6 - - + +
141A ARG* 2.9 41.8 + - - -
142A GLN* 3.0 49.6 + - - +
232A MET* 3.8 13.4 - - + +
276A PHE* 3.7 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL 3.3 16.6 - - - +
136A ALA 3.4 16.8 - - - +
137A LEU 3.5 0.2 - - - -
138A GLU* 1.3 93.4 - - + +
140A VAL* 1.3 59.9 + - - +
142A GLN* 3.9 15.3 - - - +
143A LYS* 3.8 21.5 + - - +
272A ALA* 3.4 32.8 - - + +
273A ILE* 4.1 10.8 - - + -
276A PHE* 3.6 30.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
136A ALA 4.1 15.5 - - - +
137A LEU* 2.9 10.8 + - - +
139A PRO* 1.3 76.2 - - - +
141A ARG* 1.3 60.5 + - - +
143A LYS 3.2 1.9 + - - -
144A TRP* 2.9 44.6 + - + -
146A LEU* 4.4 4.3 - - + -
258A ILE* 3.9 14.1 - - + -
260A THR* 3.8 28.9 - - + -
264A ALA* 5.1 1.1 - - + -
269A VAL* 3.8 29.8 - - + +
273A ILE* 4.3 8.3 - - + -
319A MET* 4.7 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU 2.9 14.8 + - - +
138A GLU* 2.9 39.4 + - - +
140A VAL* 1.3 76.8 - - - +
142A GLN* 1.3 70.0 + - - +
145A GLY* 3.0 27.0 + - - +
146A LEU* 3.8 28.2 - - + +
232A MET* 3.8 44.9 + - + +
234A ASP* 5.6 5.9 + - - +
237A ILE* 4.4 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLU 5.3 2.0 + - - -
111A VAL 5.8 0.4 + - - -
138A GLU* 3.0 50.2 + - - +
139A PRO* 3.9 13.7 - - - +
140A VAL 3.2 0.2 - - - -
141A ARG* 1.3 85.6 - - - +
143A LYS* 1.3 64.9 + - + +
276A PHE* 3.9 14.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PRO 3.8 7.3 + - - +
140A VAL 3.2 2.2 + - - +
142A GLN* 1.3 84.2 - - + +
144A TRP* 1.3 106.4 + - + +
145A GLY 3.8 0.2 - - - -
262A GLU* 5.5 2.1 - - - +
268A GLU* 5.3 1.4 + - - +
271A ALA* 6.2 0.6 - - - +
272A ALA* 4.1 22.2 - - + +
----------------------------------------------------------
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 VAL* 2.9 32.8 + - + +
143A LYS* 1.3 115.3 + - + +
145A GLY* 1.3 60.9 + - - +
260A THR* 4.1 5.4 - - + -
261A LYS* 2.9 24.6 + - - +
262A GLU* 3.0 31.5 + - + +
263A VAL 3.3 20.1 + - - -
264A ALA* 3.4 19.7 - - + -
265A PRO* 3.7 13.9 - - + +
268A GLU* 3.6 51.2 + - + -
269A VAL* 3.8 17.5 - - + -
272A ALA* 4.1 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A VAL 4.3 0.3 - - - +
141A ARG* 3.0 26.9 + - - -
143A LYS 3.8 0.6 - - - -
144A TRP* 1.3 83.5 - - - +
146A LEU* 1.3 65.7 + - - +
260A THR* 3.3 17.8 - - - +
261A LYS* 3.7 15.7 - - - -
----------------------------------------------------------
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