Contacts of the helix formed by residues 154 - 174 (chain A) 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 GLN 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLN* 3.0 23.0 - - - +
64A MET 2.9 24.1 - - - +
65A ASP* 3.4 23.8 - - - +
120A LYS* 3.6 12.5 + - - +
121A THR* 3.1 33.7 + - - +
122A ASP* 4.1 13.9 - - + -
150A ASN 5.9 0.4 - - - +
151A PRO* 3.0 12.9 + - + +
153A GLY* 1.3 93.5 + - - +
155A ALA* 1.3 59.2 + - - +
157A VAL* 3.1 9.3 - - + +
158A GLU* 2.9 32.7 + - - +
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Residues in contact with ALA 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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52A ASN* 3.9 6.9 - - - +
63A GLN* 3.5 0.2 + - - -
151A PRO 3.5 1.4 + - - -
152A GLN* 3.0 36.9 + - - +
153A GLY 3.5 0.6 - - - -
154A GLN* 1.3 76.9 - - - +
156A ILE* 1.3 63.5 + - - +
158A GLU* 3.6 11.8 - - - +
159A ARG* 3.0 25.3 + - - +
4I G 4.2 9.6 + - - +
5I C 4.0 23.1 - - - +
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Residues in contact with ILE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASN* 4.1 17.5 - - - +
53A PRO 4.4 5.4 - - - +
54A ARG* 4.5 16.4 - - + +
63A GLN* 2.8 26.2 + - - +
82A VAL* 3.9 27.6 - - + -
84A THR* 3.7 38.6 - - + +
87A HIS* 5.1 9.2 - - + -
155A ALA* 1.3 75.5 - - - +
157A VAL* 1.3 57.2 + - - +
159A ARG* 3.7 4.8 - - - +
160A THR* 2.7 31.0 + - - +
5I C 4.9 16.8 - - - +
6I C 5.5 3.8 - - - +
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Residues in contact with VAL 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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63A GLN* 2.9 43.1 + - + +
64A MET 4.1 0.4 - - - +
65A ASP* 3.7 19.5 - - + +
80A VAL* 4.3 8.3 - - + +
82A VAL* 3.8 19.3 - - + +
154A GLN* 3.1 36.1 - - + +
156A ILE* 1.3 74.1 - - - +
158A GLU* 1.3 55.3 + - + +
160A THR* 3.2 6.9 + - - -
161A HIS* 2.7 49.4 + - + +
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Residues in contact with GLU 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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65A ASP* 4.9 4.9 - - - +
151A PRO* 2.8 42.2 - - - +
154A GLN* 2.9 22.0 + - + +
155A ALA* 3.6 10.2 - - - +
157A VAL* 1.3 75.1 - - + +
159A ARG* 1.3 66.3 + - - +
161A HIS* 3.1 26.3 + - + +
162A GLN* 3.1 15.1 + - - +
4I G 5.3 0.2 - - - +
19J C 4.1 15.1 + - + +
20J A 3.0 52.1 + - + +
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Residues in contact with ARG 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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155A ALA 3.0 17.5 + - - +
156A ILE* 3.7 5.2 - - - +
158A GLU* 1.3 76.5 - - - +
160A THR* 1.3 62.2 + - - +
162A GLN* 3.1 45.4 + - - +
163A ASN* 2.8 39.3 + - - +
4I G 4.4 6.7 - - - +
5I C 3.4 18.8 - - - +
6I C 2.8 65.8 + - - +
7I G 2.7 30.9 + - - -
17J G 4.1 3.4 - - - +
18J G 3.5 2.6 - - - +
19J C 4.6 2.8 + - - -
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Residues in contact with THR 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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80A VAL* 4.5 1.8 - - + -
82A VAL* 3.7 22.3 - - + +
89A THR* 3.6 28.6 - - + +
156A ILE* 2.7 21.0 + - - +
157A VAL* 3.3 13.2 - - - -
158A GLU 3.2 0.2 - - - -
159A ARG* 1.3 78.6 - - - +
161A HIS* 1.3 56.7 + - - +
163A ASN* 3.0 14.7 + - + +
164A ILE* 2.8 47.6 + - + +
191A LEU* 5.9 0.4 - - + -
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Residues in contact with HIS 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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65A ASP* 4.3 12.7 + - + -
66A VAL 3.5 33.4 - - - -
67A THR* 3.9 20.7 + - + +
80A VAL* 3.5 41.5 - - + +
157A VAL* 2.7 35.3 + - + +
158A GLU* 3.1 19.3 + - + +
160A THR* 1.3 73.8 - - - +
162A GLN* 1.3 55.8 + - - +
164A ILE* 3.8 7.2 - - + +
165A LYS* 2.9 33.6 + - - +
19J C 4.9 9.3 + - - +
20J A 4.9 6.3 + - - -
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Residues in contact with GLN 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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158A GLU 3.1 7.8 + - - +
159A ARG* 3.1 29.9 + - - +
161A HIS* 1.3 76.7 - - - +
163A ASN* 1.3 57.9 + - - +
165A LYS* 3.6 7.6 - - - +
166A ALA* 3.0 30.1 + - - +
17J G 4.9 1.0 + - - -
18J G 3.0 52.7 + - - -
19J C 2.7 51.8 + - - +
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Residues in contact with ASN 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 ARG* 2.8 36.4 + - - +
160A THR* 3.0 15.9 + - + +
162A GLN* 1.3 77.3 - - - +
164A ILE* 1.3 60.2 + - + +
166A ALA* 3.4 6.0 + - - +
167A GLN* 2.9 30.6 + - - +
191A LEU* 4.4 17.1 - - + +
6I C 5.1 2.6 + - - -
7I G 3.9 28.0 + - - +
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Residues in contact with ILE 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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69A VAL* 6.1 1.6 - - + -
78A VAL* 6.0 2.9 - - + -
80A VAL* 4.1 28.3 - - + -
89A THR* 5.4 3.4 - - - +
90A PHE 5.8 0.2 - - - -
91A ALA* 4.4 10.8 - - + -
160A THR* 2.8 43.4 + - + +
161A HIS* 3.8 7.6 - - + +
163A ASN* 1.3 71.6 - - - +
165A LYS* 1.3 59.6 + - - +
167A GLN* 3.1 7.4 + - - +
168A LEU* 2.8 50.8 + - + +
184A LEU* 4.8 11.4 - - + -
187A ALA* 5.4 1.8 - - + -
188A LEU* 5.6 2.9 - - + -
191A LEU* 3.8 21.8 - - + -
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Residues in contact with LYS 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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69A VAL* 6.4 1.6 - - + -
161A HIS 2.9 18.9 + - - +
162A GLN* 3.6 8.1 - - - +
164A ILE* 1.3 78.4 - - - +
166A ALA* 1.3 56.9 + - - +
168A LEU* 3.2 11.3 + - - +
169A ASN* 2.9 49.7 + - - +
19J C 5.0 17.1 + - - -
20J A 5.0 12.0 + - - +
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A GLN 3.0 18.9 + - - +
163A ASN* 3.8 6.3 - - - +
165A LYS* 1.3 76.5 - - - +
167A GLN* 1.3 61.7 + - - +
169A ASN* 3.2 11.4 + - - +
170A LYS* 3.0 38.5 + - - +
41E PRO* 6.1 4.7 - - + -
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Residues in contact with GLN 167 (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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163A ASN 2.9 18.2 + - - +
164A ILE* 3.4 7.9 - - - +
166A ALA* 1.3 77.4 - - - +
168A LEU* 1.3 57.3 + - - +
170A LYS* 3.3 11.9 + - - +
171A LEU* 3.0 57.4 + - + +
187A ALA* 3.7 27.1 - - + -
190A VAL* 3.6 31.1 - - - +
191A LEU* 3.8 19.0 - - + +
195A ASN* 5.4 3.3 + - - -
12E HIS 3.7 9.7 + - - -
13E HIS* 4.2 11.4 - - - +
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Residues in contact with LEU 168 (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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69A VAL* 4.5 27.8 - - + -
71A GLU* 5.3 5.8 - - - +
72A PHE* 5.4 4.7 - - + -
78A VAL* 6.3 0.7 - - + -
164A ILE* 2.8 37.3 + - + +
165A LYS* 3.5 9.0 - - - +
167A GLN* 1.3 76.8 - - - +
169A ASN* 1.3 59.6 - - - +
171A LEU* 3.7 3.6 - - - +
172A GLN* 2.8 33.5 + - - +
183A LEU* 3.6 33.7 - - + +
184A LEU* 4.1 18.8 - - + -
187A ALA* 3.8 20.6 - - + -
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Residues in contact with ASN 169 (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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71A GLU* 5.2 5.4 - - - +
165A LYS* 2.9 42.2 + - - +
166A ALA* 3.2 10.7 + - - +
168A LEU* 1.3 79.4 - - - +
170A LYS* 1.3 63.5 + - + +
172A GLN* 3.9 4.5 - - - +
173A LYS* 3.0 39.7 + - - +
41E PRO* 6.4 2.9 - - + -
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Residues in contact with LYS 170 (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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166A ALA* 3.0 28.5 + - - +
167A GLN* 3.7 15.2 + - - +
169A ASN* 1.3 75.4 - - + +
171A LEU* 1.3 57.9 + - - +
173A LYS* 3.3 4.2 + - - +
174A ALA 3.0 22.9 + - - -
13E HIS* 3.0 40.9 + - + +
39E ASN* 3.5 22.8 - - - +
40E CYS* 4.0 22.3 - - - +
41E PRO* 4.1 22.4 - - + -
8I C 4.2 15.8 + - - -
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Residues in contact with LEU 171 (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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167A GLN* 3.0 36.6 + - - +
170A LYS* 1.3 77.0 - - - +
172A GLN* 1.3 64.2 + - - +
174A ALA* 3.3 14.6 + - + +
175A GLY 3.5 0.7 + - - -
177A TYR* 2.8 29.3 + - - +
183A LEU* 3.5 12.6 - - + -
186A HIS* 3.6 37.2 - - + +
187A ALA* 3.5 40.6 - - + +
11E LEU 4.6 2.2 - - - +
12E HIS 4.0 7.2 - - - +
13E HIS* 3.9 15.7 - - + -
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Residues in contact with GLN 172 (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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71A GLU* 3.5 26.5 - - - +
72A PHE* 5.0 3.1 - - - -
168A LEU 2.8 20.0 + - - +
169A ASN* 3.9 5.4 - - - +
171A LEU* 1.3 72.7 - - - +
173A LYS* 1.3 67.4 + - + +
175A GLY* 3.0 32.2 + - - +
176A LYS* 4.6 6.1 - - - +
177A TYR* 3.9 12.6 - - - +
183A LEU* 3.7 16.8 - - + +
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Residues in contact with LYS 173 (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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169A ASN* 3.0 29.2 + - - +
170A LYS 3.6 2.7 - - - +
172A GLN* 1.3 77.3 - - + +
174A ALA* 1.3 62.9 + - - +
175A GLY* 3.3 1.0 + - - -
38E PRO 5.2 0.4 - - - +
39E ASN* 3.5 49.4 + - - +
40E CYS 6.1 0.2 - - - -
41E PRO* 5.5 10.5 - - - +
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Residues in contact with ALA 174 (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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170A LYS 3.0 14.4 + - - +
171A LEU* 3.3 17.7 - - + +
172A GLN 3.1 0.6 - - - -
173A LYS* 1.3 76.1 - - - +
175A GLY* 1.3 55.7 + - - +
177A TYR* 4.7 3.4 - - - +
10E ALA 4.6 11.7 - - - +
11E LEU 5.5 2.5 - - - +
13E HIS* 3.8 15.0 - - + +
39E ASN* 3.7 11.4 - - - +
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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