Contacts of the helix formed by residues 137 - 154 (chain A) in PDB entry 3K9O
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 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLN* 2.8 19.2 + - + +
136A GLN* 1.3 83.0 - - + +
138A PRO* 1.3 67.0 - - - +
139A GLU* 3.6 8.7 + - - +
140A MET* 3.0 51.9 + - + +
141A PHE 2.9 18.5 + - - -
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Residues in contact with PRO 138 (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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134A TYR 3.7 17.7 - - - +
135A LYS 3.6 14.6 - - - +
136A GLN 3.6 3.1 - - - +
137A ASN* 1.3 90.2 - - - +
139A GLU* 1.3 62.3 + - - +
141A PHE* 3.4 7.3 + - + +
142A LYS* 3.0 23.7 + - - +
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Residues in contact with GLU 139 (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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137A ASN* 3.1 7.2 + - - +
138A PRO* 1.3 80.5 - - - +
140A MET* 1.3 62.6 + - - +
142A LYS* 3.3 21.0 + - - +
143A GLN* 2.9 51.3 + - + +
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Residues in contact with MET 140 (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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133A GLN* 3.7 16.6 - - - +
137A ASN* 3.0 37.7 + - + +
139A GLU* 1.3 72.1 - - - +
141A PHE* 1.3 61.1 + - - +
143A GLN* 3.9 2.1 - - - +
144A THR* 2.7 47.5 + - - +
162A TYR* 3.8 15.3 - - + +
187A SER* 3.3 50.7 - - - +
188A TRP* 4.0 10.1 - - + -
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Residues in contact with PHE 141 (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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50A PRO* 4.5 9.9 - - + -
51A TYR* 3.5 24.9 - + - -
80A TRP* 3.5 33.9 - + - -
82A PRO* 3.8 11.9 - - + -
130A VAL* 3.5 21.3 - - + -
133A GLN* 3.2 16.4 + - - +
134A TYR* 3.5 52.3 - + - -
137A ASN 2.9 13.1 + - - +
138A PRO* 3.7 9.6 - - + +
140A MET* 1.3 76.0 - - - +
142A LYS* 1.3 62.6 + - + +
144A THR* 3.2 1.6 + - - -
145A ALA* 2.8 35.3 + - + +
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Residues in contact with LYS 142 (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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49A THR 6.3 0.9 - - - -
50A PRO* 3.7 22.8 - - + +
138A PRO 3.0 14.0 + - - +
139A GLU* 3.6 25.4 + - - +
140A MET 3.3 0.2 - - - -
141A PHE* 1.3 84.5 - - + +
143A GLN* 1.4 70.2 + - - +
145A ALA 3.4 0.2 + - - -
146A ARG* 3.1 48.6 + - - +
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Residues in contact with GLN 143 (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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139A GLU* 2.9 41.6 + - + +
140A MET* 4.8 0.7 - - - -
142A LYS* 1.4 83.8 + - - +
144A THR* 1.3 59.2 + - - +
146A ARG* 2.9 39.8 + - - +
147A LEU* 3.0 27.2 + - - +
158A SER* 5.1 2.3 - - - +
159A SER* 5.1 15.5 - - - +
162A TYR* 3.5 29.1 - - + +
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Residues in contact with THR 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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80A TRP* 3.5 32.8 - - + +
133A GLN* 3.7 2.9 + - - +
140A MET* 2.7 33.2 + - - +
141A PHE 3.7 2.2 - - - -
143A GLN* 1.3 71.4 - - - +
145A ALA* 1.3 64.2 - - - +
147A LEU* 3.1 4.3 + - - +
148A TRP* 3.0 32.0 + - + +
162A TYR* 3.9 6.1 + - - -
184A SER* 3.5 29.2 - - - +
188A TRP* 2.8 23.5 + - + +
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Residues in contact with ALA 145 (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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50A PRO* 3.6 26.5 - - + -
51A TYR* 3.9 13.4 - - + +
80A TRP* 3.6 31.5 - - + +
141A PHE* 2.8 21.6 + - + +
144A THR* 1.3 78.4 - - - +
146A ARG* 1.3 55.5 + - - +
148A TRP* 3.3 3.5 + - - +
149A ALA* 2.9 28.2 + - - +
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Residues in contact with ARG 146 (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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50A PRO* 3.5 28.9 - - + +
52A GLU* 5.8 3.1 + - - -
142A LYS* 3.1 42.0 + - - +
143A GLN* 2.9 38.4 + - - +
144A THR 3.3 0.2 - - - -
145A ALA* 1.3 75.7 - - - +
147A LEU* 1.3 58.1 + - - +
149A ALA* 3.2 2.3 + - - +
150A HIS* 2.9 28.9 + - - +
155A ALA* 4.9 0.9 - - - +
156A PRO 4.9 1.6 - - - +
157A VAL 4.1 17.9 + - - -
158A SER* 4.1 12.5 - - - +
159A SER 6.0 0.2 - - - +
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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
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143A GLN 3.0 14.9 + - - +
144A THR* 3.1 8.3 + - - +
146A ARG* 1.3 77.2 - - - +
148A TRP* 1.3 73.0 + - + +
150A HIS* 3.2 3.9 + - - +
151A VAL* 2.8 53.5 + - + +
158A SER* 3.1 31.8 - - - +
162A TYR* 4.0 27.6 - - + -
163A THR* 4.3 14.4 - - - +
166A ILE* 4.0 15.5 - - + -
180A ILE* 4.2 7.6 - - + -
188A TRP* 3.9 17.0 - - + -
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Residues in contact with TRP 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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56A TYR* 6.1 0.2 - - - -
78A LYS* 3.8 19.4 - - + +
79A ILE* 3.5 34.1 - - + -
80A TRP* 3.4 41.7 - + + +
86A SER* 3.4 29.2 - - - -
144A THR* 3.0 31.8 + - + +
145A ALA 3.7 6.7 - - - +
147A LEU* 1.3 88.0 - - + +
149A ALA* 1.3 58.4 + - - +
151A VAL* 4.6 0.4 - - - -
152A TYR* 2.9 60.0 + + + +
180A ILE* 3.4 19.5 - - + +
181A VAL* 4.0 17.3 - - + -
184A SER* 2.8 26.9 + - - -
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Residues in contact with ALA 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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50A PRO 3.6 16.6 - - - +
51A TYR* 4.2 2.5 - - + -
56A TYR* 3.4 27.1 - - - +
145A ALA 2.9 14.6 + - - +
146A ARG* 3.2 8.0 + - - +
148A TRP* 1.3 78.2 - - - +
150A HIS* 1.3 57.5 + - - +
153A ALA* 2.9 26.1 + - - -
154A GLY 3.1 0.2 + - - -
155A ALA* 3.0 27.6 + - + -
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Residues in contact with HIS 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 ARG 2.9 15.1 + - - +
147A LEU* 3.6 4.1 - - - +
149A ALA* 1.3 80.1 - - - +
151A VAL* 1.3 74.1 + - + +
152A TYR 3.5 0.2 + - - -
154A GLY* 3.9 9.7 + - - -
155A ALA* 3.1 26.8 - - - +
156A PRO* 3.3 26.7 - - + +
157A VAL* 3.6 19.0 + - + +
158A SER* 3.4 20.5 + - - +
163A THR* 5.4 5.4 + - + -
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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
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147A LEU* 2.8 47.2 + - + +
148A TRP* 4.6 0.2 - - - -
150A HIS* 1.3 83.0 - - + +
152A TYR* 1.3 94.7 + - + +
154A GLY 5.3 0.2 + - - -
166A ILE* 5.2 3.1 - - + -
176A ARG* 5.5 6.5 - - + -
180A ILE* 3.9 16.4 - - + -
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Residues in contact with TYR 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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77A THR* 3.6 14.0 - - + +
78A LYS* 3.5 49.3 - - + +
148A TRP* 2.9 54.2 + + - +
151A VAL* 1.3 103.7 - - + +
153A ALA* 1.3 59.0 + - - +
154A GLY 3.6 1.7 + - - -
177A ASN* 2.6 40.7 + - - +
180A ILE* 3.6 22.5 - - + +
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Residues in contact with ALA 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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53A GLY 4.2 0.3 - - - +
54A GLY* 3.2 4.9 - - - -
55A ARG* 2.9 38.4 + - - +
56A TYR* 3.2 45.1 - - + +
77A THR* 3.9 2.7 - - + -
148A TRP 4.7 0.4 - - - +
149A ALA* 2.9 14.8 + - - +
152A TYR* 1.3 77.3 - - + +
154A GLY* 1.3 60.0 + - - +
155A ALA 3.5 0.2 - - - -
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Residues in contact with GLY 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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53A GLY 3.6 8.1 - - - +
149A ALA 3.1 1.6 + - - -
150A HIS 3.9 7.7 + - - -
152A TYR 3.6 3.0 + - - -
153A ALA* 1.3 77.7 - - - +
155A ALA* 1.3 64.6 + - - +
156A PRO* 4.6 1.0 - - - +
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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