Contacts of the helix formed by residues 137 - 151 (chain D) in PDB entry 2UZ1
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 HIS 137 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LEU 3.3 26.7 - - - -
105B ARG 2.9 22.3 + - - -
107B ASP* 3.7 22.4 + - + +
132D VAL* 4.2 2.7 - - + -
133D MET 4.5 2.6 + - - -
134D ALA* 2.9 37.2 + - + +
136D GLU* 1.3 83.8 - - + +
138D ILE* 1.3 65.6 + - - +
139D PRO* 3.4 1.3 - - - -
140D ARG* 3.4 31.6 + - - +
141D LEU* 3.0 41.1 + - + +
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Residues in contact with ILE 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D GLY* 3.6 32.1 - - - +
9D LEU* 3.8 7.2 - - + -
10D VAL* 3.6 39.3 - - + +
132D VAL* 4.1 20.9 - - + -
135D THR* 3.0 19.5 + - - +
137D HIS* 1.3 77.4 - - - +
139D PRO* 1.3 62.3 - - + +
141D LEU* 4.9 1.6 - - - -
142D VAL* 2.8 35.9 + - + +
159D LEU* 5.2 0.2 - - - +
161D LEU* 4.1 8.5 - - + -
165D ILE* 3.9 22.0 - - + +
166D LEU* 4.4 8.7 - - + -
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Residues in contact with PRO 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 4.0 17.0 - - + -
13D THR* 3.3 30.0 - - + +
135D THR 4.3 2.7 - - - +
136D GLU 3.7 11.2 - - - +
137D HIS 3.7 2.5 - - - -
138D ILE* 1.3 93.7 - - + +
140D ARG* 1.3 56.1 + - - +
143D MET* 3.0 27.5 + - - +
175D VAL* 4.0 11.2 - - + -
176D ILE 3.6 17.3 - - - +
177D ILE* 3.7 22.4 - - + -
178D PRO* 3.7 11.1 - - + +
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Residues in contact with ARG 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ARG 4.1 21.6 + - - +
311A LEU* 3.7 17.0 - - - +
105B ARG 4.9 0.4 + - - -
106B ASP 4.8 0.2 - - - -
107B ASP 2.7 24.2 + - - -
108B GLU* 3.1 30.7 + - - +
109B THR* 3.5 12.3 - - - +
136D GLU 5.1 2.6 + - - +
137D HIS* 3.4 46.7 + - - +
139D PRO* 1.3 80.1 - - - +
141D LEU* 1.3 69.0 + - + +
143D MET* 4.0 1.4 - - - +
144D GLN* 2.9 32.5 + - - +
147D ARG* 4.7 2.4 + - - -
176D ILE 5.3 0.4 + - - -
178D PRO* 4.4 11.8 - - + +
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Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ASP* 4.3 9.6 - - - +
108B GLU* 3.9 13.9 - - + -
128D TRP* 4.0 8.0 - - + -
130D HIS* 4.1 24.7 - - + +
132D VAL* 4.2 16.8 - - + -
137D HIS* 3.0 39.5 + - + +
138D ILE 4.1 1.6 - - - +
140D ARG* 1.3 93.9 - - + +
142D VAL* 1.3 60.2 + - - +
144D GLN* 3.6 28.1 - - - +
145D ALA* 2.9 30.1 + - - +
159D LEU* 4.4 14.9 - - + +
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Residues in contact with VAL 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D VAL* 4.6 18.4 - - + -
13D THR* 3.6 24.2 - - + -
14D LEU* 4.0 16.8 - - + +
96D LEU* 4.5 4.3 - - + -
98D LEU* 5.0 2.9 - - + -
138D ILE* 2.8 40.3 + - + +
141D LEU* 1.3 72.1 - - - +
143D MET* 1.3 62.8 + - - +
145D ALA* 3.2 5.9 + - - +
146D ILE* 3.0 39.2 + - + +
159D LEU* 3.8 23.1 - - + +
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Residues in contact with MET 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D THR* 3.7 28.7 - - + +
16D LYS* 4.6 0.9 - - + -
17D ALA* 3.8 26.0 - - + +
139D PRO 3.0 17.8 + - - +
140D ARG 4.0 2.5 - - - +
142D VAL* 1.3 77.4 - - - +
144D GLN* 1.3 63.8 + - - +
146D ILE* 3.2 8.0 + - - +
147D ARG* 3.0 43.5 + - - +
178D PRO* 3.2 36.6 - - + +
179D ASP 3.7 14.8 - - - +
180D LEU* 3.8 30.7 - - + +
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Residues in contact with GLN 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A CYS* 3.6 31.4 - - + +
310A ARG* 3.4 40.8 + - - +
108B GLU* 3.1 21.5 - - - +
128D TRP* 3.6 21.2 - - + -
140D ARG* 2.9 19.9 + - - +
141D LEU* 3.6 21.7 - - - +
142D VAL 3.3 0.2 - - - -
143D MET* 1.3 74.7 - - - +
145D ALA* 1.3 63.1 + - - +
147D ARG* 3.3 16.7 + - - +
148D ALA* 3.0 22.9 + - - +
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Residues in contact with ALA 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU* 3.7 17.7 - - + -
128D TRP* 3.9 16.8 - - + -
141D LEU 2.9 18.5 + - - +
142D VAL* 3.5 5.8 - - - +
144D GLN* 1.3 76.4 - - - +
146D ILE* 1.3 57.6 + - - +
148D ALA* 3.3 4.4 + - - +
149D ALA* 3.0 25.8 + - - +
157D VAL* 3.6 27.9 - - + +
159D LEU* 4.3 8.1 - - + -
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Residues in contact with ILE 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D THR 5.0 0.2 - - - +
14D LEU* 4.3 9.9 - - + -
17D ALA* 3.6 26.7 - - + -
19D VAL* 5.0 0.4 - - + -
67D LEU* 3.9 27.1 - - + -
96D LEU* 3.9 11.0 - - + -
142D VAL* 3.0 33.4 + - + +
143D MET* 3.6 12.6 - - - +
145D ALA* 1.3 74.3 - - - +
147D ARG* 1.3 64.9 + - - +
149D ALA* 3.2 6.6 + - - +
150D LEU* 3.0 46.6 + - + +
180D LEU* 4.0 19.3 - - + -
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Residues in contact with ARG 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ALA* 2.9 37.2 + - + +
306A CYS 2.8 22.2 + - - -
308A LEU* 3.1 25.2 + - - -
309A GLY 4.3 4.4 + - - -
310A ARG* 3.9 12.9 + - - +
140D ARG 4.7 2.8 + - - -
143D MET* 3.0 39.7 + - - +
144D GLN* 3.5 27.8 - - - +
146D ILE* 1.3 75.2 - - - +
148D ALA* 1.3 59.9 + - - +
151D SER* 2.9 32.1 + - - -
178D PRO* 5.8 1.8 - - - +
179D ASP 5.2 2.2 + - - -
180D LEU* 3.8 18.6 - - + -
181D VAL 4.3 17.1 + - - +
182D LEU* 4.1 16.4 - - + +
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Residues in contact with ALA 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A CYS* 3.4 28.2 - - - +
127D LYS* 2.8 36.6 + - + +
128D TRP* 4.4 11.9 - - + -
144D GLN 3.0 8.6 + - - +
145D ALA* 3.4 11.4 - - - +
146D ILE 3.2 0.2 - - - -
147D ARG* 1.3 76.2 - - - +
149D ALA* 1.3 59.3 + - - +
151D SER* 3.1 6.3 + - - -
157D VAL* 3.7 15.0 - - + -
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Residues in contact with ALA 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D LEU* 3.8 23.1 - - + -
94D PRO* 3.4 10.1 - - + +
95D VAL 4.4 6.5 - - - +
96D LEU* 4.9 1.1 - - - +
145D ALA 3.0 16.9 + - - +
146D ILE* 3.2 5.1 + - - +
148D ALA* 1.3 77.1 - - - +
150D LEU* 1.3 60.9 + - - +
154D ARG* 3.4 6.2 - - - -
155D GLY 3.3 41.2 + - - +
157D VAL* 3.7 10.3 - - + +
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Residues in contact with LEU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D LYS* 4.6 2.7 - - - -
67D LEU* 4.0 29.6 - - + +
94D PRO* 4.0 20.9 - - + -
146D ILE* 3.0 39.2 + - + +
149D ALA* 1.3 75.8 - - - +
151D SER* 1.3 60.3 + - - +
154D ARG* 2.8 32.4 + - + +
180D LEU* 4.1 16.4 - - + -
182D LEU* 4.4 17.0 - - + +
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Residues in contact with SER 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ASP* 5.7 0.2 + - - -
305A ALA* 3.5 23.8 + - - +
319A VAL* 5.2 8.1 - - - -
127D LYS* 2.9 22.9 + - - -
147D ARG 2.9 19.9 + - - -
148D ALA* 3.1 12.3 + - - -
149D ALA 3.3 0.2 - - - -
150D LEU* 1.3 80.9 - - - +
152D ALA* 1.3 61.9 + - - +
153D PRO 3.0 9.5 - - - +
154D ARG* 3.2 6.6 + - - +
182D LEU* 5.1 4.9 - - - -
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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) + - + + + + + -
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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