Contacts of the helix formed by residues 151 - 166 (chain C) in PDB entry 3K9L
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 GLY 151 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142C ILE* 3.8 2.8 - - - +
143C GLU 3.8 14.6 - - - -
144C THR* 3.4 12.8 - - - +
149C ARG 3.2 1.4 + - - -
150C GLN* 1.3 74.5 - - - +
152C VAL* 1.3 57.6 + - - +
153C GLU 3.6 1.6 - - - -
154C ASP* 3.3 20.9 + - - +
155C ALA 2.9 24.3 + - - -
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Residues in contact with VAL 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.7 44.6 - - + +
22C GLN* 4.2 8.5 - - + -
23C LEU* 4.2 15.5 - - + +
144C THR* 4.3 4.5 - - - -
145C SER 3.7 16.4 - - - +
146C ALA* 4.2 0.2 - - - -
149C ARG* 3.3 33.1 + - + +
150C GLN 3.2 2.8 - - - +
151C GLY* 1.3 73.7 - - - +
153C GLU* 1.3 66.3 + - - +
155C ALA* 3.2 10.5 + - - +
156C PHE* 3.3 28.5 + - + -
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Residues in contact with GLU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLN 5.9 0.4 - - - -
26A ASN* 3.0 21.9 + - - +
42A LYS* 4.9 4.1 + - - -
23C LEU* 4.4 9.9 - - + -
149C ARG* 2.8 39.5 + - - +
151C GLY 3.6 0.2 - - - -
152C VAL* 1.3 75.7 - - - +
154C ASP* 1.3 62.0 + - - +
157C TYR* 2.8 68.4 + - + +
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Residues in contact with ASP 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ILE* 4.0 15.7 - - + +
151C GLY* 3.3 19.2 + - - +
152C VAL 3.2 0.4 - - - -
153C GLU* 1.3 83.0 - - - +
155C ALA* 1.3 57.2 + - - +
157C TYR* 4.7 2.7 - - - -
158C THR* 2.5 41.1 + - - +
161C ARG* 5.5 2.2 - - - +
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Residues in contact with ALA 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 5.9 1.1 - - + -
79C LEU* 3.7 17.1 - - + +
112C VAL* 4.4 2.4 - - - +
114C VAL* 3.9 25.6 - - + -
142C ILE* 4.0 14.1 - - + +
144C THR* 4.1 11.4 - - + -
151C GLY 2.9 13.6 + - - +
152C VAL* 3.2 9.6 + - - +
154C ASP* 1.3 76.8 - - - +
156C PHE* 1.3 67.6 + - + +
158C THR* 3.8 2.4 - - - -
159C LEU 3.1 16.3 + - - -
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Residues in contact with PHE 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 3.9 23.8 - - + +
8C VAL* 4.2 13.2 - - + -
19C LEU* 3.8 32.8 - - + -
20C THR* 4.2 16.2 - - - -
23C LEU* 3.5 40.2 - - + -
53C LEU* 5.0 2.2 - - + -
55C ILE* 4.1 12.3 - - + -
79C LEU* 3.6 32.1 - - + -
152C VAL* 3.3 28.4 + - + +
153C GLU 4.3 0.2 - - - +
155C ALA* 1.3 78.8 - - + +
157C TYR* 1.3 65.7 + - + +
159C LEU* 3.1 8.4 + - + +
160C VAL* 3.0 30.5 + - - +
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Residues in contact with TYR 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LEU* 4.4 19.2 - - + +
44C VAL* 4.4 14.6 - - + +
45C VAL 4.1 13.6 + - - -
46C ILE* 3.9 40.7 - - + +
53C LEU* 4.9 7.6 - - + -
153C GLU* 2.8 50.4 + - + +
154C ASP* 4.2 1.6 - - - +
156C PHE* 1.3 74.1 - - + +
158C THR* 1.3 60.1 + - - +
160C VAL* 3.3 7.9 + - - +
161C ARG* 3.0 56.1 + - - +
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Residues in contact with THR 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C VAL* 4.0 5.8 - - + -
140C PRO* 3.9 33.9 - - + -
142C ILE* 4.0 15.2 - - + +
154C ASP* 2.5 29.5 + - - +
155C ALA 3.8 3.6 - - - -
157C TYR* 1.3 77.8 - - - +
159C LEU* 1.3 56.0 + - - +
161C ARG* 3.2 21.6 + - + +
162C GLU* 2.9 28.5 + - + +
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Residues in contact with LEU 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 3.9 30.1 - - + -
77C GLY* 3.8 12.3 - - - +
78C PHE 3.7 48.0 - - - +
79C LEU* 3.7 16.2 - - + +
110C PRO 4.0 1.3 - - - -
111C MET* 3.9 23.1 - - - +
112C VAL* 3.8 9.8 - - + +
155C ALA 3.1 13.2 + - - +
156C PHE* 3.1 11.0 + - + +
158C THR* 1.3 72.5 - - - +
160C VAL* 1.3 67.1 + - - +
162C GLU* 3.1 3.4 + - + +
163C ILE* 3.0 27.3 + - + +
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Residues in contact with VAL 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C TYR* 4.0 23.1 - - + -
6C LEU* 4.4 8.7 - - + -
46C ILE* 3.8 19.7 - - + -
53C LEU* 3.6 30.5 - - + -
156C PHE 3.0 15.8 + - - +
157C TYR 3.7 7.0 - - - +
158C THR 3.3 0.2 - - - -
159C LEU* 1.3 76.2 - - - +
161C ARG* 1.3 58.1 + - - +
163C ILE* 3.2 9.9 + - - +
164C ARG* 2.9 57.5 + - - +
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Residues in contact with ARG 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ILE* 4.1 11.1 - - + +
47C ASP* 2.8 43.4 + - - +
154C ASP* 4.8 2.4 + - - +
157C TYR* 3.0 53.8 + - - +
158C THR* 3.4 21.9 + - + +
159C LEU 3.1 0.2 - - - -
160C VAL* 1.3 77.9 - - + +
162C GLU* 1.3 61.8 + - + +
164C ARG* 3.3 12.3 + - - +
165C GLN* 3.0 40.5 + - - +
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Residues in contact with GLU 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C PRO* 4.2 12.3 - - + -
111C MET 4.3 6.2 + - - +
112C VAL* 4.2 6.1 - - + -
138C GLY 5.2 3.8 - - - +
139C ILE* 5.6 1.2 - - - +
140C PRO* 3.7 39.4 - - + +
158C THR* 2.9 18.4 + - + +
159C LEU* 3.1 13.7 + - + +
161C ARG* 1.3 75.8 - - - +
163C ILE* 1.3 61.6 + - - +
165C GLN* 3.2 26.5 + - - +
166C HIS* 2.6 51.7 + - - -
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Residues in contact with ILE 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C TYR* 3.7 28.3 - - + -
6C LEU* 3.3 34.1 - - + -
76C GLU* 4.0 26.0 - - + +
77C GLY* 3.8 16.6 - - - +
110C PRO* 3.8 24.2 - - + -
159C LEU* 3.0 17.5 + - + +
160C VAL* 3.5 7.0 - - - +
162C GLU* 1.3 74.4 - - - +
164C ARG* 1.3 65.7 + - - +
166C HIS* 3.2 20.1 + - - +
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Residues in contact with ARG 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C TYR* 2.6 27.9 + - + +
46C ILE* 2.9 36.2 + - - +
47C ASP* 4.1 9.9 + - - +
49C GLU* 2.9 48.7 + - - +
51C CYS* 3.7 21.2 - - - -
160C VAL* 2.9 28.5 + - - +
161C ARG* 3.3 11.3 + - - +
163C ILE* 1.3 76.0 - - - +
165C GLN* 1.3 61.7 + - + +
166C HIS 3.6 3.8 + - - +
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Residues in contact with GLN 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C ARG* 3.0 32.3 + - + +
162C GLU* 3.2 32.8 + - - +
163C ILE 3.2 0.2 - - - -
164C ARG* 1.3 78.3 - - + +
166C HIS* 1.3 65.6 + - - +
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Residues in contact with HIS 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ASP* 3.2 39.8 + - - -
109C VAL 4.8 1.0 + - - -
110C PRO* 3.8 35.9 - - + +
162C GLU* 2.6 48.5 + - - +
163C ILE 3.2 15.0 + - - +
164C ARG 4.0 4.2 - - - +
165C GLN* 1.3 88.3 - - + +
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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