Contacts of the helix formed by residues 137 - 154 (chain A) in PDB entry 1K89
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 ASP 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LYS 4.0 0.2 + - - -
136A SER* 1.3 73.7 - - - +
138A ARG* 1.3 59.1 + - - +
140A VAL* 3.5 2.6 + - - +
141A MET* 3.0 26.0 + - - +
171A ARG* 3.2 34.0 + - - +
175A TYR* 2.3 31.5 + - - -
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Residues in contact with ARG 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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67A ASP* 3.8 13.2 - - - +
136A SER* 3.1 4.8 + - - +
137A ASP* 1.3 83.7 + - - +
139A GLU* 1.3 61.6 + - - +
141A MET* 3.3 33.4 + - + +
142A ARG* 3.1 48.7 + - - +
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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
----------------------------------------------------------
64A TRP* 4.1 15.6 - - + -
66A ASP* 3.1 19.1 - - - +
67A ASP* 2.8 43.3 + - - +
68A ASN* 4.6 1.6 + - - +
130A PHE* 4.9 1.6 - - - -
134A GLY 4.2 2.6 - - - +
135A LYS* 3.3 21.7 - - + +
136A SER* 2.8 45.4 + - - +
138A ARG* 1.3 74.1 - - - +
140A VAL* 1.3 65.2 + - - +
142A ARG* 3.3 11.0 + - - +
143A PHE* 3.0 22.9 + - - +
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Residues in contact with VAL 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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94A PHE* 6.0 0.2 - - + -
130A PHE* 4.4 18.6 - - + -
132A PRO* 4.7 8.3 - - + +
135A LYS* 3.7 22.0 - - + +
136A SER 2.9 20.6 + - - +
137A ASP 3.7 4.3 - - - +
139A GLU* 1.3 75.8 - - - +
141A MET* 1.3 59.0 + - - +
143A PHE* 3.3 1.6 + - - +
144A CYS* 2.9 33.3 + - - -
171A ARG* 3.8 27.4 - - - +
172A GLU* 3.5 34.1 - - + +
175A TYR* 4.4 3.6 - - + -
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Residues in contact with MET 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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137A ASP 3.0 17.9 + - - +
138A ARG* 3.5 31.2 - - - +
139A GLU 3.2 0.2 - - - -
140A VAL* 1.3 78.1 - - - +
142A ARG* 1.3 76.3 + - + +
144A CYS* 3.3 2.1 + - - +
145A GLN* 3.0 60.7 + - - +
175A TYR* 3.5 42.6 - - + -
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Residues in contact with ARG 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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64A TRP* 4.5 4.9 - - + +
65A GLU* 2.9 43.3 + - - +
66A ASP* 3.0 29.4 - - - +
67A ASP* 2.8 26.0 + - - +
138A ARG* 3.1 39.2 + - - +
139A GLU* 3.3 11.0 + - - +
141A MET* 1.3 89.2 - - + +
143A PHE* 1.3 62.8 + - - +
145A GLN* 3.4 11.5 + - - +
146A ALA* 3.0 23.4 + - - +
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Residues in contact with PHE 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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62A VAL* 3.5 27.1 - - + -
64A TRP* 3.5 33.6 - + + +
74A ASN* 4.1 3.1 - - + -
94A PHE* 3.7 33.2 - + - -
128A SER* 3.4 26.2 - - - -
130A PHE* 3.5 50.0 - + + -
139A GLU 3.0 16.8 + - - +
140A VAL 3.6 4.5 - - - +
142A ARG* 1.3 78.7 - - - +
144A CYS* 1.3 60.2 + - - +
146A ALA* 3.1 2.8 + - - +
147A PHE* 2.8 40.4 + + + +
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Residues in contact with CYS 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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94A PHE* 4.2 12.3 - - - -
140A VAL* 2.9 27.5 + - - +
141A MET 3.7 4.3 - - - +
143A PHE* 1.3 79.5 - - - +
145A GLN* 1.3 56.7 + - - +
147A PHE* 3.5 7.3 - - - +
148A MET* 2.9 31.5 + - - +
172A GLU* 3.9 42.4 - - - -
175A TYR* 3.8 14.8 - - + -
176A MET* 3.7 20.8 - - + +
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Residues in contact with GLN 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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141A MET* 3.0 49.8 + - + +
142A ARG* 3.7 9.5 - - - +
143A PHE 3.2 0.2 - - - -
144A CYS* 1.3 74.3 - - - +
146A ALA* 1.3 60.8 + - - +
148A MET 3.5 0.2 + - - -
149A THR* 2.5 35.3 + - - -
175A TYR* 4.5 8.8 + - - +
178A GLY 6.2 0.2 - - - -
179A GLN* 3.6 41.8 + - + +
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Residues in contact with ALA 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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61A ARG 5.6 1.2 - - - +
62A VAL* 3.8 12.1 - - + +
63A PRO* 3.4 27.3 - - + +
64A TRP* 4.5 3.8 - - + -
142A ARG 3.0 18.0 + - - +
143A PHE 3.7 3.4 - - - +
145A GLN* 1.3 75.9 - - - +
147A PHE* 1.3 63.8 + - - +
149A THR* 3.3 19.0 + - - -
150A GLU* 3.8 6.1 + - - +
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Residues in contact with PHE 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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60A PHE* 3.6 36.9 - + - -
62A VAL* 3.8 10.7 - - + +
76A GLY* 3.8 5.2 - - - -
77A TYR 4.6 2.5 - - - -
92A LEU* 4.0 26.5 - - + -
94A PHE* 4.0 16.6 - + - -
127A GLY 3.5 29.6 - - - -
128A SER* 4.2 1.1 - - - -
143A PHE* 2.8 40.9 + + + +
144A CYS* 3.5 4.5 - - - +
146A ALA* 1.3 76.6 - - - +
148A MET* 1.3 60.2 + - - +
150A GLU 3.4 3.3 + - - -
151A LEU* 3.1 46.0 + - + +
176A MET* 3.9 16.2 - - - -
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Residues in contact with MET 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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144A CYS 2.9 18.5 + - - +
147A PHE* 1.3 73.0 - - - +
149A THR* 1.3 65.2 + - - +
150A GLU 3.0 2.7 - - - -
151A LEU* 3.6 16.2 - - + +
152A TYR* 2.9 49.7 + - + +
155A ILE* 3.9 19.7 - - + -
176A MET* 3.5 47.6 - - + +
179A GLN* 4.1 11.4 - - + -
180A TYR* 3.8 24.2 - - + +
183A ILE* 4.3 1.2 - - + +
192A LEU* 4.2 15.5 - - + -
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Residues in contact with THR 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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145A GLN 2.5 24.2 + - - -
146A ALA* 3.6 9.8 - - - -
147A PHE 3.3 0.4 - - - -
148A MET* 1.3 76.6 - - - +
150A GLU* 1.3 58.1 + - - +
152A TYR* 3.3 21.3 - - + -
153A ARG* 3.7 6.1 + - - +
179A GLN* 3.0 18.5 + - - +
183A ILE* 3.8 16.4 - - + -
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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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58A ILE* 4.9 1.2 - - - +
60A PHE* 3.5 46.5 - - + +
61A ARG 5.3 2.9 - - - +
146A ALA 3.8 4.5 + - - +
147A PHE 3.4 3.5 + - - +
148A MET 3.0 0.2 - - - -
149A THR* 1.3 80.1 - - - +
151A LEU* 1.3 66.5 + - - +
152A TYR 3.1 2.9 + - - -
153A ARG* 3.1 42.2 + - - +
154A HIS* 2.8 29.6 + - - +
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Residues in contact with LEU 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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58A ILE* 5.9 0.2 - - + -
60A PHE* 4.1 19.7 - - + -
77A TYR 5.3 0.2 - - - +
78A ARG* 4.1 25.6 - - + -
92A LEU* 4.7 9.0 - - + -
147A PHE* 3.1 42.2 + - + +
148A MET* 4.2 21.8 - - + -
150A GLU* 1.3 80.8 - - - +
152A TYR* 1.3 65.1 + - - +
154A HIS* 2.9 24.4 + - + -
155A ILE* 3.6 30.7 + - + +
162A PRO* 4.6 9.6 - - + -
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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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148A MET* 2.9 25.7 + - + +
149A THR* 3.3 28.0 - - + -
150A GLU 3.1 1.4 + - - -
151A LEU* 1.3 77.8 - - - +
153A ARG* 1.3 100.9 + - + +
154A HIS 3.3 0.7 + - - -
155A ILE* 3.4 23.4 + - - +
180A TYR* 3.7 24.1 + - + -
183A ILE* 3.7 32.3 - - + +
184A VAL* 3.7 22.4 - - + -
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Residues in contact with ARG 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 THR 3.7 16.6 + - - -
150A GLU* 3.1 36.6 + - - +
151A LEU 2.9 1.4 + - - -
152A TYR* 1.3 117.7 + - + +
154A HIS* 1.3 82.8 + - + +
155A ILE 3.6 1.8 - - - +
159A ILE* 5.9 1.6 - - - +
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Residues in contact with HIS 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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56A ARG* 5.7 2.4 - - - -
58A ILE* 3.6 53.0 - - + +
60A PHE* 5.5 0.2 - + - -
80A GLN* 3.0 22.7 + - - +
150A GLU* 2.8 41.3 + - + -
151A LEU* 2.9 17.7 + - + +
153A ARG* 1.3 97.1 + - + +
155A ILE* 1.3 62.0 + - + +
159A ILE* 3.6 13.5 - - - +
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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
------------------------------------------------------------
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