Contacts of the helix formed by residues 149 - 166 (chain A) in PDB entry 3KM6
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 149 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU* 3.2 22.9 - - - -
79A TYR* 4.4 0.9 - - - -
80A GLY* 4.6 2.9 - - - -
89A VAL* 3.7 23.5 - - - +
143A ILE* 4.4 4.2 - - - +
144A VAL* 5.0 4.4 + - - +
147A GLN 4.5 3.8 - - - -
148A ILE* 1.3 75.1 - - - +
150A PHE* 1.3 64.0 + - - +
151A ALA* 3.4 19.6 + - - +
152A ASP* 2.9 26.7 + - - +
153A TYR* 3.3 14.9 - - - -
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Residues in contact with PHE 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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20A LEU* 3.8 13.7 - - + -
69A LEU* 3.5 40.6 - - + +
70A ARG* 3.5 25.1 - - + -
73A GLY* 4.1 9.4 - - - -
78A LEU* 3.0 28.2 + - - +
79A TYR* 3.5 25.4 - + - -
89A VAL* 3.4 24.7 - - + -
90A ASP* 3.7 13.7 - - - -
93A ASN* 3.6 35.7 - - + -
149A SER* 1.3 71.6 - - - +
151A ALA* 1.3 63.1 + - - +
153A TYR* 3.3 22.4 + - - +
154A ASN* 3.3 12.6 + - - +
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Residues in contact with ALA 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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89A VAL* 3.7 28.0 - - + +
92A VAL* 3.9 21.2 - - + +
93A ASN* 3.9 17.3 - - + +
96A VAL* 4.8 0.5 - - - +
143A ILE* 4.2 5.6 - - + -
149A SER* 3.1 12.4 + - - +
150A PHE* 1.3 79.5 - - - +
152A ASP* 1.3 59.7 + - - +
154A ASN* 3.8 0.7 - - - +
155A LEU* 2.8 33.1 + - - +
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Residues in contact with ASP 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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142A PHE* 3.5 14.7 - - - +
143A ILE* 3.0 27.3 + - - +
144A VAL 4.9 0.5 + - - -
147A GLN 4.2 0.3 - - - +
148A ILE* 3.5 22.9 - - + -
149A SER* 2.9 36.3 + - - +
151A ALA* 1.3 77.7 - - - +
153A TYR* 1.3 58.0 + - - +
156A LEU* 2.8 32.5 + - - +
179A TYR* 2.5 32.3 + - - +
183A LEU* 4.0 7.6 - - + +
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Residues in contact with TYR 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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16A ALA* 3.6 20.4 - - - +
19A MET* 3.1 24.3 - - + +
20A LEU* 3.6 46.9 - - + -
23A ASP* 2.7 43.0 + - + +
24A GLN* 3.0 20.0 + - - -
69A LEU* 5.2 0.7 - - + -
78A LEU* 4.3 7.4 - - + -
148A ILE* 3.4 25.1 - - + +
149A SER 3.3 28.5 - - - -
150A PHE* 3.3 5.4 + - - +
152A ASP* 1.3 76.5 - - - +
154A ASN* 1.3 57.3 + - - +
156A LEU* 4.4 3.4 - - + -
157A ASP* 3.0 24.3 + - - +
183A LEU* 6.0 0.7 - - + -
189A LEU* 4.4 10.8 - - + -
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Residues in contact with ASN 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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16A ALA* 3.6 11.9 - - - +
66A ASN* 3.6 15.4 - - - +
69A LEU* 3.7 15.8 - - + +
93A ASN* 2.9 35.5 + - - +
96A VAL* 3.4 20.4 - - + +
97A GLU* 4.7 3.2 + - - +
100A ARG* 2.9 31.7 + - - +
150A PHE 3.3 5.6 + - - +
151A ALA 3.9 3.8 - - - +
153A TYR* 1.3 76.1 - - - +
155A LEU* 1.3 64.9 + - - +
157A ASP 3.4 0.7 + - - -
158A LEU* 3.0 23.4 + - - +
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Residues in contact with LEU 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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92A VAL* 4.8 1.6 - - + -
96A VAL* 3.8 18.5 - - + +
129A PHE* 3.8 39.5 - - + -
143A ILE* 3.6 35.4 - - + -
151A ALA 2.8 22.9 + - - +
152A ASP 3.8 2.0 - - - +
154A ASN* 1.3 71.1 - - - +
156A LEU* 1.3 66.6 + - - +
158A LEU* 3.2 8.6 + - + +
159A LEU* 2.9 46.7 + - + +
176A LEU* 4.6 4.0 - - + -
179A TYR* 3.6 23.3 - - + +
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Residues in contact with LEU 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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19A MET* 4.0 15.0 - - + -
152A ASP 2.8 22.7 + - - +
153A TYR* 3.7 6.3 - - + +
155A LEU* 1.3 72.3 - - - +
157A ASP* 1.3 63.2 + - - +
159A LEU* 3.2 7.9 + - - +
160A LEU* 3.0 36.8 + - + +
179A TYR* 4.5 4.4 - - + +
180A VAL* 3.8 43.5 - - + +
183A LEU* 4.0 22.7 - - + -
184A SER* 4.0 11.2 - - - +
189A LEU* 3.8 29.2 - - + -
193A LEU* 5.2 0.9 - - + -
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Residues in contact with ASP 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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11A ARG* 5.7 0.9 - - - +
12A GLY 4.2 1.0 - - - +
15A ALA* 3.3 30.9 - - - +
16A ALA* 4.2 6.4 + - + -
19A MET* 3.6 15.7 - - + +
100A ARG* 3.0 36.2 + - - +
153A TYR 3.0 17.7 + - - +
154A ASN 3.8 0.4 - - - +
156A LEU* 1.3 75.1 - - - +
158A LEU* 1.3 65.0 + - - +
160A LEU* 3.1 7.5 + - - +
161A ILE* 3.1 36.3 + - - +
198A TYR* 4.8 8.8 + - - -
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Residues in contact with LEU 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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96A VAL* 3.8 20.4 - - + +
99A LEU* 3.8 26.2 - - + -
100A ARG* 3.6 39.4 - - + +
126A LEU* 5.2 4.9 - - + -
129A PHE* 4.3 17.0 - - + -
154A ASN 3.0 14.3 + - - +
155A LEU* 3.2 16.1 + - + +
157A ASP* 1.3 75.6 - - - +
159A LEU* 1.3 62.1 + - + +
161A ILE* 3.3 12.7 - - + +
162A HIS* 2.8 52.2 + - + +
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Residues in contact with LEU 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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126A LEU* 4.1 18.8 - - + -
129A PHE* 5.7 0.4 - - + -
155A LEU* 2.9 39.4 + - + +
156A LEU* 3.7 4.9 - - - +
158A LEU* 1.3 75.3 - - + +
160A LEU* 1.3 63.8 + - - +
162A HIS* 3.3 5.2 + - - +
163A GLU* 3.0 28.5 + - - +
170A LEU* 3.6 29.4 - - + +
176A LEU* 3.8 32.3 - - + +
179A TYR* 4.0 12.1 - - + -
180A VAL* 3.7 29.8 - - + -
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Residues in contact with LEU 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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19A MET* 4.3 14.8 - - - -
156A LEU* 3.0 38.2 + - + +
157A ASP* 3.1 7.8 + - - +
159A LEU* 1.3 76.5 - - - +
161A ILE* 1.3 64.8 + - + +
163A GLU* 3.5 7.3 + - + +
164A VAL* 3.4 24.8 + - - +
180A VAL* 3.8 27.4 - - + -
184A SER* 4.4 6.3 - - - +
193A LEU* 4.6 11.4 - - + -
198A TYR* 4.0 22.0 - - - +
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Residues in contact with ILE 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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11A ARG* 6.4 0.9 - - + -
100A ARG* 3.8 26.2 - - + +
103A TYR* 3.8 42.7 + - + +
157A ASP* 3.1 27.1 + - - +
158A LEU* 3.3 21.3 - - + +
160A LEU* 1.3 76.6 - - + +
162A HIS* 1.3 69.0 + - + +
164A VAL* 3.3 10.0 + - - +
165A LEU* 2.9 26.0 + - - +
198A TYR* 6.1 0.7 - - - +
203A ILE* 3.7 29.3 - - + +
209A GLN* 4.4 1.0 - - - +
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Residues in contact with HIS 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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99A LEU* 4.1 6.8 - - + +
103A TYR* 3.7 18.4 - + + -
118A TYR* 2.7 37.1 + + - -
122A LEU* 3.5 32.2 - - + +
126A LEU* 5.1 7.0 - - + -
158A LEU* 2.8 55.4 + - + +
159A LEU* 3.3 5.3 + - - +
161A ILE* 1.3 76.7 - - + +
163A GLU* 1.3 55.1 + - - +
164A VAL 3.2 0.4 - - - -
165A LEU* 3.7 9.4 - - + +
166A ALA* 2.7 37.8 + - - +
169A CYS* 3.5 16.4 - - - -
170A LEU* 6.0 0.7 - - + -
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Residues in contact with GLU 163 (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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159A LEU 3.0 14.9 + - - +
160A LEU* 3.8 8.7 - - + +
161A ILE 3.4 0.2 - - - -
162A HIS* 1.3 75.5 - - - +
164A VAL* 1.3 59.5 + - + +
166A ALA 3.9 2.0 - - - -
167A PRO* 3.2 29.5 - - - +
168A GLY* 2.8 27.9 + - - -
169A CYS* 3.3 5.8 + - - -
170A LEU* 2.8 55.3 + - + +
171A ASP 4.4 0.3 + - - -
180A VAL* 6.4 1.1 - - + -
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Residues in contact with VAL 164 (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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11A ARG* 6.1 0.7 - - - +
160A LEU 3.4 14.3 + - - +
161A ILE 3.3 7.9 + - - +
162A HIS 3.2 0.6 - - - -
163A GLU* 1.3 79.5 - - + +
165A LEU* 1.3 64.7 + - - +
166A ALA 3.4 0.3 + - - -
167A PRO* 3.9 9.8 - - - +
203A ILE* 4.0 15.9 - - + -
209A GLN* 3.6 51.7 - - + +
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Residues in contact with LEU 165 (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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103A TYR* 4.2 9.2 - - + -
106A LEU* 3.9 13.5 - - + -
107A ILE* 4.4 6.1 - - + -
111A TYR* 3.7 27.6 - - + -
115A LYS* 3.4 40.3 + - - -
118A TYR* 3.5 39.0 - - + -
119A VAL* 4.9 6.2 - - + +
122A LEU* 5.3 0.4 - - + -
161A ILE 2.9 14.9 + - - +
162A HIS* 3.2 15.0 + - + +
164A VAL* 1.3 78.9 - - - +
166A ALA* 1.3 61.6 + - + +
167A PRO* 3.8 4.1 - - - +
209A GLN* 3.1 25.1 + - - +
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Residues in contact with ALA 166 (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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119A VAL* 4.1 26.0 - - + -
122A LEU* 4.1 22.4 - - + -
162A HIS 2.7 14.4 + - - +
163A GLU* 3.7 1.0 - - - -
165A LEU* 1.3 78.6 - - + +
167A PRO* 1.3 68.8 - - - +
168A GLY 3.3 0.2 + - - -
169A CYS* 3.0 26.6 + - + -
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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