Contacts of the helix formed by residues 146 - 161 (chain A) in PDB entry 3K9W
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 PHE 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LEU* 5.2 1.1 + - + -
14A THR 5.1 1.8 - - - -
15A ARG* 3.6 39.5 - - + +
18A GLU* 3.6 46.4 - - + -
57A VAL* 3.8 33.7 - - + -
123A TYR* 6.1 1.3 - - - -
145A VAL* 1.3 77.7 - - - +
147A PRO* 1.4 80.2 - - + +
148A SER* 3.2 4.5 - - - +
149A VAL* 2.9 18.1 + - + +
150A GLU* 3.0 10.1 + - - +
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Residues in contact with PRO 147 (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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15A ARG* 4.0 11.9 - - - +
142A SER* 6.3 4.9 - - - -
146A PHE* 1.4 94.8 - - + +
148A SER* 1.3 63.0 + - - +
150A GLU* 3.2 11.0 + - + +
151A LYS* 3.1 32.8 + - - +
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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
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53A ILE 5.0 0.2 + - - -
56A GLU* 3.7 26.2 + - - +
57A VAL* 3.6 24.4 + - - +
146A PHE* 4.4 3.3 - - - +
147A PRO* 1.3 79.0 - - - +
149A VAL* 1.3 64.3 + - - +
151A LYS* 3.4 16.9 + - - +
152A TRP* 3.3 27.2 + - - -
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Residues in contact with VAL 149 (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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12A PRO* 3.6 38.4 - - + -
13A LEU* 3.7 16.8 - - + +
53A ILE* 3.8 14.6 - - + +
57A VAL* 3.7 28.3 - - + -
145A VAL* 3.8 13.7 - - + -
146A PHE* 2.9 17.4 + - + +
148A SER* 1.3 76.3 - - - +
150A GLU* 1.3 64.5 + - - +
152A TRP* 3.2 10.4 + - + +
153A LEU* 3.0 23.1 + - + +
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Residues in contact with GLU 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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135A ALA* 5.6 1.2 - - - +
139A GLY 4.7 5.4 - - - +
140A ASP* 3.4 17.0 - - - +
141A VAL* 3.0 40.5 + - - +
142A SER* 3.5 9.7 + - - +
145A VAL* 3.8 7.9 - - + +
146A PHE 3.0 11.4 + - - +
147A PRO* 3.2 13.7 + - + +
149A VAL* 1.3 75.9 - - - +
151A LYS* 1.3 57.6 + - + +
153A LEU* 3.2 6.8 + - - +
154A THR* 2.9 56.3 + - - +
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Residues in contact with LYS 151 (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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147A PRO* 3.1 26.1 + - - +
148A SER* 3.4 15.1 - - - +
149A VAL 3.2 0.2 - - - -
150A GLU* 1.3 77.4 - - + +
152A TRP* 1.3 58.6 + - + +
154A THR* 3.5 5.8 + - - -
155A GLU* 3.0 41.9 + - - +
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Residues in contact with TRP 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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45A PHE* 3.7 19.8 - + + -
49A GLU* 3.8 31.0 - - + -
52A LYS* 3.9 41.1 - - + -
53A ILE* 3.4 36.0 - - + +
56A GLU* 3.0 32.8 + - - -
148A SER 3.3 22.3 + - - -
149A VAL* 3.2 8.8 + - - +
151A LYS* 1.3 77.6 - - + +
153A LEU* 1.3 59.9 + - - +
155A GLU* 3.3 9.9 + - + +
156A LYS* 2.9 32.6 + - + +
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Residues in contact with LEU 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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12A PRO* 4.3 17.3 - - + -
44A PHE* 4.2 13.9 - - + -
45A PHE* 3.7 27.8 - - + -
131A VAL* 4.2 12.8 - - + -
132A ARG* 4.9 8.1 - - + -
135A ALA* 4.0 23.8 - - + -
141A VAL* 3.6 29.6 - - + -
145A VAL* 4.3 6.3 - - + -
149A VAL 3.0 17.5 + - - +
150A GLU* 3.2 9.6 + - - +
152A TRP* 1.3 75.0 - - - +
154A THR* 1.3 58.1 + - - +
156A LYS* 3.3 1.1 + - - +
157A VAL* 2.9 37.1 + - - +
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Residues in contact with THR 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 GLU* 2.9 33.8 + - - +
151A LYS* 3.8 6.3 - - - -
153A LEU* 1.3 76.5 - - - +
155A GLU* 1.3 66.6 + - + +
157A VAL* 3.9 4.7 - - - +
158A ALA* 3.0 26.0 + - + +
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Residues in contact with GLU 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 LYS* 3.0 27.0 + - - +
152A TRP* 4.0 10.3 - - + +
154A THR* 1.3 81.0 - - + +
156A LYS* 1.3 56.2 + - - +
158A ALA* 3.4 5.7 + - - +
159A ALA* 3.0 29.3 + - - +
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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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44A PHE* 3.2 48.2 + - + -
45A PHE* 3.7 17.2 - - + +
46A SER* 4.1 4.9 - - - +
49A GLU* 2.8 39.3 + - - +
152A TRP* 2.9 19.2 + - + +
155A GLU* 1.3 72.7 - - - +
157A VAL* 1.3 66.4 + - - +
159A ALA* 3.2 5.2 + - + +
160A MET* 3.0 52.8 + - + +
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Residues in contact with VAL 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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44A PHE* 4.0 20.2 - - + -
135A ALA* 3.6 36.1 - - + +
136A GLN* 3.9 21.5 - - + +
138A GLY* 5.4 2.7 - - - +
153A LEU 2.9 23.5 + - - +
154A THR* 3.9 5.4 - - - +
156A LYS* 1.3 77.3 - - - +
158A ALA* 1.3 62.1 + - - +
160A MET* 3.5 4.1 + - - +
161A ALA* 3.3 21.5 + - - +
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Residues in contact with ALA 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 THR* 3.0 21.0 + - + +
155A GLU* 3.7 5.4 - - - +
157A VAL* 1.3 77.6 - - - +
159A ALA* 1.3 63.0 + - - +
161A ALA* 3.5 19.5 + - - +
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Residues in contact with ALA 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 GLU 3.0 17.3 + - - +
156A LYS* 3.2 7.6 + - + +
158A ALA* 1.3 79.2 - - - +
160A MET* 1.3 77.6 + - + +
161A ALA 3.4 4.3 + - - -
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Residues in contact with MET 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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44A PHE* 4.6 11.7 - - + -
156A LYS* 3.0 47.3 + - + +
157A VAL* 4.1 4.7 - - - +
158A ALA 3.4 0.2 - - - -
159A ALA* 1.3 92.2 - - + +
161A ALA* 1.3 61.5 + - - +
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Residues in contact with ALA 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 VAL* 3.3 15.6 + - + +
158A ALA* 3.8 14.1 - - - +
159A ALA 3.2 5.8 - - - -
160A MET* 1.3 80.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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