Contacts of the helix formed by residues 137 - 154 (chain F) in PDB entry 2J3W
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 LEU 137 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47F VAL* 6.1 0.8 - - - +
51F GLN* 3.6 23.6 + - - +
136F THR* 1.3 74.2 - - - +
138F ASN* 1.3 59.3 + - - +
139F CYS 3.4 2.2 - - - -
140F ALA* 3.2 8.1 + - + +
141F ALA* 2.8 30.1 + - - +
162F VAL* 3.9 14.5 - - + +
163F HIS* 3.8 35.2 - - - +
164F TRP* 3.6 47.5 - - + +
168F THR* 4.0 27.6 - - + +
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Residues in contact with ASN 138 (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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33F PHE* 3.7 5.0 - - + -
37F VAL* 3.9 27.2 - - + +
41F GLN* 5.3 1.6 - - - +
47F VAL* 4.8 3.7 - - - +
50F LEU* 3.1 34.7 - - - +
51F GLN* 4.1 8.5 - - - +
54F LEU* 3.3 27.0 - - + +
136F THR* 2.9 34.3 + - - +
137F LEU* 1.3 75.3 - - - +
139F CYS* 1.3 65.5 + - - +
141F ALA* 3.3 1.8 + - - -
142F PHE 3.2 17.2 + - - -
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Residues in contact with CYS 139 (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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29F PHE* 5.8 1.6 - - - -
33F PHE* 3.6 24.5 - - + -
98F PHE* 4.2 9.6 - - - -
123F LEU* 3.7 23.6 - - + -
124F ILE* 4.0 28.7 - - + +
127F TYR* 4.3 11.0 - - - -
136F THR* 4.8 3.4 + - - +
137F LEU 3.4 0.2 - - - -
138F ASN* 1.3 78.3 - - - +
140F ALA* 1.3 54.3 + - - +
142F PHE* 3.5 5.1 + - - +
143F THR* 2.8 42.1 + - - -
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Residues in contact with ALA 140 (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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123F LEU* 3.4 15.8 - - + +
136F THR 5.3 0.6 + - - -
137F LEU* 3.2 17.8 + - + +
138F ASN 3.1 0.2 - - - -
139F CYS* 1.3 77.7 - - - +
141F ALA* 1.3 54.6 + - - +
143F THR* 3.3 2.4 + - - -
144F GLY 2.7 29.6 + - - -
162F VAL* 3.2 24.0 - - + +
168F THR* 3.7 29.8 - - + -
170F LEU* 3.7 2.9 - - + +
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Residues in contact with ALA 141 (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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51F GLN* 3.4 44.0 - - + +
54F LEU* 4.2 1.6 - - + -
55F ALA* 3.3 15.4 - - + +
137F LEU 2.8 15.6 + - - +
138F ASN 3.7 5.8 - - - +
139F CYS 3.3 0.2 - - - -
140F ALA* 1.3 74.1 - - - +
142F PHE* 1.3 65.3 + - - +
144F GLY* 3.3 1.2 + - - -
145F GLY 2.9 17.3 + - - -
162F VAL* 3.7 13.4 - - + +
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Residues in contact with PHE 142 (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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18D LEU* 5.0 2.9 - - + -
22D THR* 3.7 36.3 - - + -
25D ALA* 5.3 0.4 - - + -
29F PHE* 4.3 15.9 - + - -
33F PHE* 3.5 30.5 - + + -
36F MET* 4.8 3.8 - - + -
54F LEU* 3.4 28.8 - - + +
57F MET* 4.0 12.6 - - + -
58F GLY* 3.6 23.1 - - - -
61F VAL* 4.0 14.6 - - + -
138F ASN 3.2 6.8 + - - +
139F CYS* 3.6 10.5 - - - +
141F ALA* 1.3 77.2 - - - +
143F THR* 1.3 67.3 + - - +
145F GLY* 2.9 12.6 + - - -
146F ILE* 3.0 29.7 + - + +
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Residues in contact with THR 143 (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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94F TRP* 3.9 27.4 - - + -
97F LEU* 4.2 11.5 - - + +
98F PHE* 3.3 35.4 - - + -
123F LEU* 3.9 2.3 - - + +
139F CYS* 2.8 22.5 + - - -
140F ALA* 3.4 7.9 - - - -
142F PHE* 1.3 82.5 - - - +
144F GLY* 1.3 57.3 + - - +
146F ILE* 2.9 15.8 + - - +
147F VAL* 2.8 28.1 + - + +
170F LEU* 4.2 5.2 - - + -
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Residues in contact with GLY 144 (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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55F ALA* 5.2 0.9 - - - -
140F ALA 2.7 21.3 + - - -
141F ALA 3.3 2.9 + - - -
142F PHE 3.2 0.2 - - - -
143F THR* 1.3 72.8 - - - +
145F GLY* 1.3 57.7 + - - +
147F VAL* 4.4 0.9 - - - -
148F GLU* 2.9 30.1 + - - +
160F VAL* 3.7 29.9 - - - +
162F VAL* 4.7 2.5 - - - -
170F LEU* 4.3 10.5 - - - -
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Residues in contact with GLY 145 (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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55F ALA* 3.2 29.4 - - - +
59F GLN* 3.1 31.5 - - - +
141F ALA 2.9 8.5 + - - -
142F PHE 2.9 7.9 + - - -
144F GLY* 1.3 77.0 - - - +
146F ILE* 1.3 62.1 + - - +
148F GLU* 3.5 3.0 + - - +
149F ALA 3.3 10.9 + - - -
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Residues in contact with ILE 146 (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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18D LEU* 4.6 3.4 - - + -
58F GLY* 3.3 21.8 - - - +
61F VAL* 3.4 20.2 - - + -
62F GLY* 3.7 13.4 - - - -
65F LEU* 4.3 10.1 - - + -
93F VAL* 4.6 1.3 - - + -
97F LEU* 4.3 33.0 - - + -
142F PHE* 3.0 31.9 + - + +
143F THR* 2.9 11.5 + - - +
145F GLY* 1.3 78.3 - - - +
147F VAL* 1.3 62.4 + - + +
149F ALA* 3.4 3.5 + - - +
150F ILE* 3.1 37.5 + - + +
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Residues in contact with VAL 147 (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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89F ILE* 3.8 33.9 - - + -
93F VAL* 4.9 8.3 - - + -
94F TRP* 4.5 2.7 - - + -
143F THR* 2.8 22.9 + - + +
144F GLY* 3.8 6.5 - - - +
146F ILE* 1.3 76.2 - - + +
148F GLU* 1.3 66.2 + - - +
150F ILE* 3.4 5.4 + - - +
151F LEU* 3.1 44.0 + - + +
160F VAL* 4.1 11.4 - - + -
170F LEU* 4.0 17.5 - - + -
172F ILE* 4.6 10.5 - - + -
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Residues in contact with GLU 148 (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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59F GLN* 3.5 25.5 + - - +
144F GLY 2.9 18.0 + - - +
145F GLY* 3.9 6.7 - - - +
146F ILE 3.4 0.2 - - - -
147F VAL* 1.3 76.2 - - - +
149F ALA* 1.3 59.2 + - - +
151F LEU* 3.8 2.8 - - - +
152F THR* 2.8 41.7 + - + +
158F ALA* 3.3 24.8 - - - +
159F LYS* 3.5 9.8 - - - +
160F VAL* 2.7 45.2 + - + +
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Residues in contact with ALA 149 (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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59F GLN* 3.2 48.8 + - + +
62F GLY 4.9 0.7 - - - -
63F ALA 3.8 9.0 - - - +
145F GLY 3.3 5.2 + - - +
146F ILE 3.7 4.3 - - - +
147F VAL 3.2 0.2 - - - -
148F GLU* 1.3 75.8 - - - +
150F ILE* 1.3 57.1 + - - +
152F THR* 2.9 7.6 + - - -
153F HIS* 2.7 47.9 + - + +
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Residues in contact with ILE 150 (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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62F GLY* 3.5 19.5 - - - +
65F LEU* 4.7 11.4 - - + -
66F LEU* 3.7 24.4 - - + +
69F LEU* 5.2 1.3 - - + -
85F ILE* 5.3 0.7 - - + -
88F PHE* 3.7 27.1 - - + -
89F ILE* 3.8 13.7 - - + -
93F VAL* 3.6 34.5 - - + -
146F ILE* 3.1 28.2 + - + +
147F VAL 3.4 3.8 + - - +
149F ALA* 1.3 79.1 - - - +
151F LEU* 1.3 59.9 + - + +
154F SER* 3.0 35.8 + - - +
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Residues in contact with LEU 151 (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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85F ILE* 3.7 35.7 - - + +
86F LEU* 5.0 2.0 - - + -
89F ILE* 3.8 21.5 - - + -
147F VAL* 3.1 35.2 + - + +
148F GLU* 3.8 2.9 - - - +
150F ILE* 1.3 74.9 - - - +
152F THR* 1.3 62.9 + - + +
154F SER* 3.1 13.6 + - - -
156F PHE* 2.8 36.0 + - + +
158F ALA* 4.5 5.8 - - + -
160F VAL* 4.6 2.7 - - + -
172F ILE* 3.5 34.1 - - + -
174F PHE* 4.0 11.7 - - + -
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Residues in contact with THR 152 (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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12C HIS* 5.1 3.3 - - - -
59F GLN* 5.2 2.2 + - - +
148F GLU* 2.8 33.9 + - + +
149F ALA* 2.9 20.3 + - - -
151F LEU* 1.3 73.2 - - + +
153F HIS* 1.3 64.4 + - - +
155F GLY* 3.0 18.5 + - - -
156F PHE 3.8 7.7 + - - -
157F PRO* 3.7 9.2 - - + +
158F ALA* 3.5 34.1 - - - +
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Residues in contact with HIS 153 (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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12C HIS* 3.8 26.6 - + - -
79C GLY* 3.1 32.8 + - - +
80C HIS* 3.5 5.5 + - - +
117C PRO* 4.6 23.0 - - + +
118C ASN* 5.7 1.8 - - - -
63F ALA* 3.8 30.8 + - + +
66F LEU* 3.4 21.3 - - + -
149F ALA* 2.7 39.3 + - + +
152F THR* 1.3 82.4 + - - +
154F SER* 1.3 57.2 + - - +
155F GLY 3.1 3.2 + - - -
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Residues in contact with SER 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C TRP* 4.2 0.5 - - - -
78C ALA 3.7 10.3 + - - -
80C HIS* 3.0 19.6 + - - -
66F LEU* 3.9 16.5 - - - +
78F ARG* 5.7 0.3 - - - +
79F GLU 4.7 1.6 - - - +
85F ILE* 3.5 23.8 - - - +
150F ILE* 3.0 22.6 + - - +
151F LEU 3.3 7.9 - - - -
152F THR 3.1 0.6 - - - -
153F HIS* 1.3 75.7 - - - +
155F GLY* 1.3 58.3 + - - +
156F PHE* 3.2 25.1 - - - -
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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