Contacts of the helix formed by residues 143 - 162 (chain A) in PDB entry 6DWZ
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 143 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LEU 3.9 1.2 + - - -
142A PRO* 1.3 79.3 - - - +
144A PRO* 1.3 67.8 - - - +
145A ILE* 2.6 33.4 + - - +
146A THR* 2.5 27.0 + - - -
147A LEU* 3.4 4.7 + - - +
7G G 3.3 22.2 + - - -
8G T 4.1 19.1 - - - -
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Residues in contact with PRO 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A SER* 1.3 84.9 - - - +
145A ILE* 1.3 59.9 + - - +
146A THR 3.1 0.7 - - - -
147A LEU* 3.6 7.1 - - + +
148A SER* 2.7 29.1 + - - -
109E PHE* 3.5 35.1 - - + +
110E SER* 3.7 11.4 - - - +
112E VAL* 3.7 10.5 - - + -
113E SER* 3.0 27.8 - - - +
7F C 6.6 0.2 - - + -
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Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A SER* 2.6 29.4 + - - +
144A PRO* 1.3 77.7 - - - +
146A THR* 1.3 57.4 + - - +
148A SER* 3.6 9.1 - - - +
149A ARG* 3.0 68.1 + - + +
7F C 4.8 21.9 - - + +
8F A 3.8 21.3 - - - +
9F A 3.7 25.1 - - - +
7G G 4.4 0.4 - - - +
8G T 3.6 23.6 - - + +
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Residues in contact with THR 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PRO* 3.1 10.1 - - - +
143A SER* 2.5 28.3 + - - +
145A ILE* 1.3 75.7 - - - +
147A LEU* 1.3 53.3 + - - +
149A ARG* 3.1 22.4 + - - +
150A LYS* 2.6 38.6 + - - +
95E ILE* 4.5 11.7 - - + +
6G T 3.6 35.9 - - + +
7G G 3.0 27.2 + - + +
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PRO* 4.5 6.3 - - + -
143A SER 3.4 7.3 + - - +
144A PRO* 3.3 10.2 + - + +
146A THR* 1.3 76.7 + - - +
148A SER* 1.3 65.9 + - - +
150A LYS* 4.0 0.8 - - - +
151A VAL* 3.0 31.0 + - + +
95E ILE* 3.7 17.7 - - + +
98E CYS* 4.1 15.9 - - + +
99E ALA* 3.3 38.8 - - + +
102E VAL* 4.7 11.9 - - + -
109E PHE* 4.6 12.1 - - + +
112E VAL* 3.3 38.6 - - + -
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Residues in contact with SER 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PRO 2.7 20.6 + - - -
145A ILE* 3.6 13.3 - - - +
146A THR 3.3 0.2 - - - -
147A LEU* 1.3 74.4 - - - +
149A ARG* 1.3 66.2 + - - +
151A VAL* 3.2 6.4 - - - +
152A THR* 3.2 23.0 + - - -
593A THR* 4.3 7.4 + - - +
109E PHE* 3.6 19.4 - - - -
6F A 5.8 0.7 - - - -
7F C 3.0 30.5 + - - -
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Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE* 3.0 50.6 + - + +
146A THR* 3.1 20.6 + - + +
148A SER* 1.3 77.1 - - - +
150A LYS* 1.3 67.3 + - - +
151A VAL 3.0 1.1 - - - -
152A THR* 2.9 19.5 + - - +
153A SER* 3.0 17.4 + - - +
9F A 4.6 0.8 - - - +
10F C 5.0 1.2 - - - +
6G T 3.8 20.7 - - - +
7G G 3.0 46.1 + - - -
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Residues in contact with LYS 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A THR 2.6 21.3 + - - +
147A LEU* 4.0 6.1 - - - +
149A ARG* 1.3 70.9 - - - +
151A VAL* 1.3 58.4 + - - +
153A SER* 3.0 12.7 + - - -
154A ASP* 2.9 70.9 + - + +
157A GLU* 4.0 9.1 + - - -
92E LYS 5.4 1.3 - - - +
95E ILE* 3.2 47.1 - - + +
96E GLU* 4.3 13.7 - - + +
99E ALA* 4.2 9.9 - - + -
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Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU* 3.0 25.6 + - + +
148A SER* 3.2 8.7 - - - +
149A ARG 3.0 0.2 - - - -
150A LYS* 1.3 77.4 - - - +
152A THR* 1.3 56.2 + - - +
154A ASP* 4.8 0.9 - - - -
155A ALA* 3.1 24.1 + - - +
593A THR* 4.7 2.7 - - + -
596A SER* 3.7 3.7 - - - -
597A LEU* 3.7 38.1 - - + +
600A LEU* 3.4 13.0 - - + +
99E ALA* 3.9 23.1 - - + -
102E VAL* 4.7 1.3 - - + -
103E VAL* 4.2 17.3 - - + -
109E PHE* 4.3 12.8 - - + -
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Residues in contact with THR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A SER* 3.2 13.6 + - - -
149A ARG* 2.9 11.0 + - - -
151A VAL* 1.3 76.6 - - - +
153A SER* 1.3 57.6 + - - +
155A ALA* 3.4 5.4 - - - +
156A LYS* 3.0 46.6 + - + +
592A GLN* 4.5 18.9 - - + +
593A THR* 4.7 12.6 + - - -
596A SER* 4.0 18.2 + - - +
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Residues in contact with SER 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ARG* 3.0 14.0 + - - +
150A LYS* 3.0 22.4 + - - -
152A THR* 1.3 72.5 - - - +
154A ASP* 1.3 56.8 + - - +
155A ALA 2.9 0.7 - - - -
156A LYS* 2.9 11.5 + - - +
157A GLU* 2.6 39.1 + - - +
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Residues in contact with ASP 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LYS* 2.9 41.4 + - + +
151A VAL* 4.8 0.4 - - - -
153A SER* 1.3 72.6 - - - +
155A ALA* 1.3 55.8 + - - +
157A GLU* 3.3 12.6 - - - +
158A LYS* 2.8 71.0 + - - +
600A LEU* 3.7 14.7 - - + +
604A TYR* 3.4 13.5 + - - -
96E GLU* 3.5 23.9 - - - +
100E GLN* 5.4 0.9 + - - +
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A VAL 3.1 21.1 + - - +
152A THR 3.4 7.0 - - - +
153A SER 2.9 0.6 - - - -
154A ASP* 1.3 77.7 - - - +
156A LYS* 1.3 65.4 + - + +
158A LYS* 3.7 0.5 + - - -
159A LYS* 3.0 31.9 + - + +
596A SER* 3.4 29.2 - - - +
599A PHE* 4.5 4.8 - - + -
600A LEU* 3.6 15.4 - - + +
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Residues in contact with LYS 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A THR* 3.0 37.0 + - + +
153A SER* 2.9 11.4 + - - +
155A ALA* 1.3 71.1 - - + +
157A GLU* 1.3 69.4 + - - +
159A LYS* 3.4 11.6 + - - +
160A ALA* 3.3 19.6 + - - +
592A GLN* 5.2 6.3 - - - -
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Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LYS* 4.0 10.6 + - - -
153A SER* 2.6 16.4 + - - +
154A ASP* 3.2 28.0 + - - +
156A LYS* 1.3 77.3 - - - +
158A LYS* 1.3 79.0 + - + +
159A LYS 2.8 4.5 + - - -
160A ALA* 3.0 2.3 + - - +
161A LEU* 3.0 21.4 + - + +
96E GLU* 4.8 2.3 - - - +
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Residues in contact with LYS 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ASP* 2.8 57.7 + - - +
157A GLU* 1.3 87.5 + - + +
159A LYS* 1.3 58.8 + - - +
160A ALA 3.5 0.2 - - - -
161A LEU* 3.8 15.0 - - + -
162A ILE* 3.2 30.1 + - - +
599A PHE* 4.1 7.3 - - + -
600A LEU* 4.4 3.8 - - + -
603A PHE* 3.3 49.2 - - + -
604A TYR* 4.0 17.5 - - + -
96E GLU* 4.2 6.4 + - - -
100E GLN* 6.1 0.4 - - - +
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Residues in contact with LYS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ALA* 3.0 23.2 + - + +
156A LYS* 3.6 11.4 - - - +
157A GLU 2.8 0.6 + - - -
158A LYS* 1.3 78.3 - - - +
160A ALA* 1.3 58.9 + - - +
162A ILE* 4.9 0.2 - - - +
163A SER* 2.9 26.3 + - - -
209A LEU 4.7 2.2 + - - +
234A GLN* 3.0 49.7 - - - +
235A PHE* 3.5 29.8 - - + -
595A ASP* 4.8 13.5 + - - +
599A PHE* 3.4 33.4 - - + -
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Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LYS 3.3 7.7 + - - +
157A GLU 3.0 6.8 + - - +
159A LYS* 1.3 76.7 - - - +
161A LEU* 1.3 71.5 + - - +
163A SER* 3.2 18.2 - - - -
164A ARG* 4.1 1.6 + - - +
234A GLN 5.0 5.8 + - - +
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLU* 3.0 17.8 + - + +
158A LYS* 3.7 12.8 - - + +
160A ALA* 1.3 81.1 - - - +
162A ILE* 1.3 83.3 - - + +
163A SER 3.2 1.6 + - - -
164A ARG* 3.6 12.8 + - - +
603A PHE* 3.9 18.6 - - + -
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Residues in contact with ILE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LYS 3.2 16.7 + - - +
159A LYS 5.2 1.3 - - - +
161A LEU* 1.3 103.0 - - + +
163A SER* 1.3 61.0 + - - +
164A ARG 2.9 6.4 + - - +
165A GLU* 3.1 19.1 + - + +
166A ILE* 3.0 43.9 + - + +
198A TYR* 5.3 0.4 - - - +
207A LEU* 4.8 10.8 - - + -
235A PHE* 5.4 1.6 - - + -
599A PHE* 4.8 6.3 - - + -
603A PHE* 3.5 13.5 - - + -
607A PHE* 3.3 42.2 - - + -
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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