Contacts of the helix formed by residues 150 - 171 (chain F) in PDB entry 3JCA
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 150 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F LYS* 5.3 9.8 - - - +
148F PRO* 4.0 5.3 + - + +
149F TYR* 1.3 77.2 - - - +
151F PRO* 1.3 62.7 - - - +
152F GLN* 2.9 53.3 + - - +
153F GLY* 3.1 5.4 + - - +
154F GLN* 2.8 38.4 + - - +
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Residues in contact with PRO 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F TYR 4.4 2.0 - - - +
150F ASN* 1.3 90.7 - - - +
152F GLN* 1.3 57.0 + - + +
154F GLN* 3.1 20.5 - - + +
155F ALA* 2.8 31.0 + - - +
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Residues in contact with GLN 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150F ASN* 2.9 31.6 + - - +
151F PRO* 1.3 68.3 - - + +
153F GLY* 1.3 63.4 + - - +
155F ALA* 3.2 7.4 + - - +
156F ILE* 3.1 27.6 + - - +
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Residues in contact with GLY 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F GLN* 4.2 15.0 - - - +
120F LYS* 4.6 12.0 - - - +
150F ASN* 3.1 8.4 + - - +
152F GLN* 1.3 75.5 - - - +
154F GLN* 1.3 64.9 + - - +
156F ILE* 3.2 17.9 + - - +
157F VAL* 3.2 25.2 + - - +
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Residues in contact with GLN 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F TYR* 3.8 30.6 - - + +
150F ASN 2.8 24.3 + - - +
151F PRO* 3.1 28.4 - - + +
153F GLY* 1.3 77.2 - - - +
155F ALA* 1.3 50.1 + - - +
157F VAL* 3.2 11.4 - - + +
158F GLU* 2.7 39.9 + - + +
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Residues in contact with ALA 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F PRO 2.8 23.0 + - - +
152F GLN* 3.5 6.3 - - - +
154F GLN* 1.3 70.2 - - - +
156F ILE* 1.3 66.9 + - + +
158F GLU* 4.1 6.5 - - - -
159F ARG* 2.8 50.0 + - + +
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Residues in contact with ILE 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F GLN* 4.1 20.6 - - + +
82F VAL* 4.0 27.6 - - + -
84F THR* 4.1 28.3 - - + +
87F HIS* 5.2 17.3 - - + +
152F GLN* 3.1 17.0 + - + +
153F GLY* 3.2 16.6 + - - +
155F ALA* 1.3 76.6 - - - +
157F VAL* 1.3 55.1 + - - +
159F ARG* 4.1 3.6 - - - +
160F THR* 2.6 36.8 + - - +
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Residues in contact with VAL 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F GLN* 3.4 34.8 - - + +
64F MET 5.0 0.2 - - - -
65F ASP* 3.5 39.3 - - + +
80F VAL* 6.2 1.6 - - + -
82F VAL* 5.7 3.6 - - + -
153F GLY 3.2 8.3 + - - +
154F GLN* 3.2 19.1 - - + +
156F ILE* 1.3 76.0 - - + +
158F GLU* 1.3 60.5 + - - +
160F THR* 3.5 6.0 - - - -
161F HIS* 2.8 41.1 + - + +
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Residues in contact with GLU 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F GLN* 2.7 25.5 + - + +
155F ALA* 3.9 6.1 - - - +
157F VAL* 1.3 72.0 - - + +
159F ARG* 1.3 67.0 + - + +
161F HIS* 3.9 9.3 - - - +
162F GLN* 2.9 61.9 + - - +
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Residues in contact with ARG 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F ALA* 2.8 36.3 + - + +
156F ILE* 4.1 2.5 - - - +
158F GLU* 1.3 77.6 - - + +
160F THR* 1.3 58.9 + - - +
162F GLN* 3.4 9.5 + - - +
163F ASN* 2.8 46.1 + - - +
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Residues in contact with THR 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F VAL* 3.9 7.6 - - + -
82F VAL* 3.6 24.7 - - + +
87F HIS 5.5 0.2 + - - -
89F THR* 3.6 37.0 + - + +
156F ILE* 2.6 24.5 + - - +
157F VAL* 3.5 8.5 - - - +
158F GLU 3.2 0.2 - - - -
159F ARG* 1.3 76.4 - - - +
161F HIS* 1.3 58.6 + - - +
163F ASN* 3.2 7.6 + - - +
164F ILE* 2.9 42.7 + - + +
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Residues in contact with HIS 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F ASP* 2.8 37.7 + - + +
66F VAL 4.9 0.4 + - - -
67F THR* 4.0 32.8 - - - +
80F VAL* 4.0 29.6 - - + +
157F VAL* 2.8 33.2 + - + +
158F GLU* 3.9 10.8 - - - +
160F THR* 1.3 73.9 - - + +
162F GLN* 1.3 59.0 + - + +
164F ILE* 3.4 8.0 + - - +
165F LYS* 2.9 49.4 + - + +
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Residues in contact with GLN 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F GLU* 2.9 53.3 + - - +
159F ARG* 3.7 8.5 - - - +
161F HIS* 1.3 78.1 - - + +
163F ASN* 1.3 54.9 + - - +
165F LYS* 3.4 6.5 + - - +
166F ALA* 2.8 36.2 + - - +
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Residues in contact with ASN 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F ARG* 2.8 34.9 + - - +
160F THR* 3.6 6.1 - - - +
162F GLN* 1.3 75.7 - - - +
164F ILE* 1.3 67.2 + - + +
166F ALA* 3.5 7.5 - - - +
167F GLN 3.0 17.7 + - - -
191F LEU* 3.7 25.5 - - + +
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Residues in contact with ILE 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F VAL* 6.1 2.0 - - + -
78F VAL* 5.5 3.6 - - + -
80F VAL* 4.2 18.2 - - + -
89F THR* 3.9 16.2 - - + -
91F ALA* 4.6 7.4 - - + -
160F THR* 2.9 40.7 + - + +
161F HIS* 3.7 9.9 - - - +
163F ASN* 1.3 75.9 - - + +
165F LYS* 1.3 59.4 - - + +
167F GLN* 3.2 5.5 + - - +
168F LEU* 2.9 47.2 + - + +
184F LEU* 4.2 16.2 - - + -
187F ALA* 4.8 0.4 - - + +
188F LEU* 4.7 2.0 - - + -
191F LEU* 3.8 21.0 - - + +
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Residues in contact with LYS 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F THR* 4.0 22.4 + - - -
68F HIS 5.1 6.5 + - - -
69F VAL* 4.8 18.2 - - + +
71F GLU* 5.8 6.7 - - - +
161F HIS* 2.9 30.8 + - + +
162F GLN* 3.9 5.8 - - - +
164F ILE* 1.3 76.0 - - + +
166F ALA* 1.3 56.3 + - - +
168F LEU* 3.5 16.3 - - + +
169F ASN* 2.7 47.5 + - - +
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Residues in contact with ALA 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F GLN 2.8 23.2 + - - +
163F ASN* 3.5 10.3 - - - +
164F ILE 3.2 0.2 - - - -
165F LYS* 1.3 73.4 - - - +
167F GLN* 1.3 56.6 + - - +
169F ASN* 3.2 10.5 + - - +
170F LYS* 2.9 40.1 + - - +
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Residues in contact with GLN 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F HIS 2.9 24.8 + - - +
13F HIS 4.4 0.3 - - - +
163F ASN 3.0 13.8 + - - +
164F ILE 3.6 6.7 - - - +
166F ALA* 1.3 73.5 - - - +
168F LEU* 1.3 66.0 + - - +
170F LYS* 3.1 28.4 + - - +
171F LEU* 3.0 46.2 + - + +
187F ALA* 3.5 32.5 - - + +
190F VAL* 3.7 26.8 - - - +
191F LEU* 4.1 11.6 - - + +
195F ASN* 4.7 4.3 + - - -
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Residues in contact with LEU 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F VAL* 4.8 18.4 - - + -
72F PHE* 4.8 12.8 - - + -
164F ILE* 2.9 37.3 + - + +
165F LYS* 3.5 14.4 - - + +
167F GLN* 1.3 74.6 - - - +
169F ASN* 1.3 64.0 + - - +
171F LEU* 3.2 12.6 + - - +
172F GLN* 2.9 28.2 + - - +
183F LEU* 3.6 30.5 - - + -
184F LEU* 4.1 16.8 - - + -
187F ALA* 3.8 19.5 - - + -
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Residues in contact with ASN 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F ASN* 4.7 6.0 - - - +
71F GLU* 4.7 11.6 - - - +
165F LYS* 2.7 32.7 + - - +
166F ALA* 3.4 8.8 - - - +
168F LEU* 1.3 74.4 - - - +
170F LYS* 1.3 64.9 + - + +
172F GLN* 3.0 28.4 + - - +
173F LYS* 4.2 2.9 + - - +
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Residues in contact with LYS 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F HIS* 2.9 50.9 + - + -
14F GLN 5.2 1.2 - - - -
15F ASN* 5.4 2.6 - - - +
39F ASN* 2.7 53.3 + - - +
40F CYS* 4.2 13.2 - - - +
41F PRO* 5.1 4.0 - - - -
166F ALA* 2.9 25.5 + - - +
167F GLN* 3.3 31.2 + - - +
169F ASN* 1.3 77.4 - - - +
171F LEU* 1.3 57.7 + - - +
172F GLN 3.2 4.3 + - - -
173F LYS* 3.4 8.1 + - - +
174F ALA* 4.6 0.9 + - - +
195F ASN* 5.4 4.0 + - - +
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Residues in contact with LEU 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F LEU 4.5 8.3 - - - +
13F HIS* 5.0 5.6 - - + -
167F GLN* 3.0 34.6 + - - +
168F LEU* 3.2 4.0 + - - +
169F ASN 3.2 0.6 - - - -
170F LYS* 1.3 74.3 - - - +
172F GLN* 1.3 58.4 + - - +
173F LYS 3.1 5.8 - - - -
174F ALA* 3.2 33.3 + - + +
175F GLY* 3.4 3.5 + - - -
177F TYR* 3.4 21.9 - - - +
183F LEU* 3.5 43.5 - - + +
186F HIS* 3.8 19.7 - - + +
187F ALA* 3.8 21.8 - - + +
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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
------------------------------------------------------------
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