Contacts of the helix formed by residues 169 - 182 (chain F) in PDB entry 2JG7
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 VAL 169 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92F LEU* 5.2 0.2 - - + -
99F LEU* 4.5 11.7 - - + -
103F VAL* 3.5 21.1 - - + -
117F GLU* 2.6 19.1 + - + +
118F VAL* 4.4 22.7 - - + -
121F TYR* 3.8 24.7 - - + -
168F PRO* 1.3 73.5 - - - +
170F ALA* 1.3 58.9 + - - +
171F VAL 3.5 1.1 + - - -
172F TYR* 3.5 7.8 + - - +
173F GLY* 3.0 23.2 + - - -
197F THR* 3.5 25.6 - - + -
201F VAL* 3.9 18.4 - - + -
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Residues in contact with ALA 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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117F GLU* 2.9 40.8 + - + +
120F GLU* 4.0 19.1 - - + -
121F TYR* 5.1 3.7 - - - +
167F PHE* 4.4 11.9 - - + -
169F VAL* 1.3 72.0 - - - +
171F VAL* 1.3 56.8 + - - +
173F GLY* 3.1 2.9 + - - +
174F TRP* 2.7 49.5 + - + +
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Residues in contact with VAL 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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161F ILE* 5.5 0.2 - - + -
163F THR* 3.7 17.0 - - + -
164F ALA* 5.6 1.6 - - + +
167F PHE* 3.6 32.8 + - + +
169F VAL 3.5 0.4 - - - -
170F ALA* 1.3 76.2 - - - +
172F TYR* 1.3 64.7 + - - +
174F TRP* 3.4 20.5 + - + +
175F ASN* 2.8 36.1 + - - +
244F THR* 3.2 44.9 - - + +
478F GLU* 4.0 5.4 - - - +
1510F NAD 4.7 8.1 - - + +
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Residues in contact with TYR 172 (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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121F TYR* 3.8 20.9 - + - -
161F ILE* 3.8 24.9 - - + -
163F THR* 3.9 7.8 - - + +
167F PHE 4.9 0.8 + - - -
168F PRO 4.6 0.6 + - - +
169F VAL 3.5 7.9 + - - +
170F ALA 3.3 0.2 - - - -
171F VAL* 1.3 78.7 - - - +
173F GLY* 1.3 53.0 + - - +
175F ASN* 3.0 4.5 + - - +
176F ASN* 2.6 59.0 + - + +
186F CYS* 4.5 3.9 - - + +
188F TRP* 3.3 83.8 - + + +
201F VAL* 3.9 15.7 - - + -
202F THR* 5.6 2.2 + - - -
205F VAL* 4.8 5.9 - - + +
219F CYS* 3.8 22.2 + - - +
220F SER 4.8 0.3 + - - -
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Residues in contact with GLY 173 (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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121F TYR* 3.5 38.3 - - - -
124F VAL* 4.0 6.7 - - - -
169F VAL 3.0 11.3 + - - -
170F ALA 3.1 4.2 + - - -
172F TYR* 1.3 76.9 - - - +
174F TRP* 1.3 61.2 + - - +
175F ASN 3.1 0.2 + - - -
176F ASN* 3.7 0.2 - - - +
177F ALA* 3.0 30.3 + - - +
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Residues in contact with TRP 174 (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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120F GLU* 3.8 38.8 + - + +
121F TYR* 5.5 0.2 - - - +
124F VAL* 3.7 30.3 - - + +
167F PHE* 6.0 7.6 - + - -
170F ALA* 2.7 28.0 + - + +
171F VAL* 3.7 24.5 - - + +
173F GLY* 1.3 72.6 - - - +
175F ASN* 1.3 61.4 + - - +
178F ILE* 3.4 27.2 + - - +
462F GLU 6.4 1.3 - - - -
463F ILE* 4.1 19.0 - - + +
467F PHE* 4.5 32.3 - + + -
478F GLU* 3.9 35.4 - - + -
479F SER* 4.0 18.8 + - - +
487F TYR* 4.4 2.6 + - - -
1510F NAD 5.4 1.8 - + - -
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Residues in contact with ASN 175 (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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161F ILE* 4.0 25.0 - - + +
171F VAL* 2.8 26.3 + - - +
172F TYR 3.0 7.0 + - - +
174F TRP* 1.3 76.7 - - - +
176F ASN* 1.3 59.7 + - - +
178F ILE* 3.5 0.7 + - - -
179F ALA* 2.9 34.7 + - - +
242F SER* 2.9 29.7 + - - -
244F THR* 4.9 0.2 + - - -
265F LEU* 4.6 0.5 - - - +
478F GLU* 2.7 27.7 + - - +
487F TYR* 2.7 31.3 + - + -
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Residues in contact with ASN 176 (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 VAL* 6.3 0.2 - - - +
88F ILE* 4.0 11.9 - - - +
121F TYR* 2.6 31.5 + - - +
125F CYS* 5.9 0.4 - - - -
161F ILE* 4.5 0.8 - - - +
172F TYR* 2.6 48.6 + - + +
173F GLY 3.2 1.8 + - - +
175F ASN* 1.3 73.7 - - - +
177F ALA* 1.3 64.7 + - - +
180F LEU* 2.9 47.4 + - - +
186F CYS* 3.8 14.9 - - - -
205F VAL* 4.8 1.6 - - - +
219F CYS* 3.5 16.6 - - - -
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Residues in contact with ALA 177 (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 VAL* 4.0 23.6 - - + +
121F TYR* 4.8 0.2 - - - -
124F VAL* 3.8 33.7 - - + +
125F CYS* 4.2 8.7 - - - -
128F ALA* 4.1 2.9 - - + -
173F GLY 3.0 16.2 + - - +
174F TRP 4.7 0.7 - - - +
176F ASN* 1.3 80.7 - - - +
178F ILE* 1.3 58.3 + - - +
181F THR* 2.7 33.8 + - - -
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Residues in contact with ILE 178 (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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124F VAL* 4.8 7.2 - - + -
127F TYR* 4.6 7.0 - - + -
128F ALA* 4.4 11.0 - - + -
131F LEU* 3.7 27.6 - - + -
174F TRP 3.4 19.7 + - - +
175F ASN 3.5 2.5 + - - +
176F ASN 3.3 0.2 - - - -
177F ALA* 1.3 75.9 - - - +
179F ALA* 1.3 65.3 + - - +
181F THR* 3.2 5.0 + - - -
182F CYS* 2.9 29.3 + - - -
479F SER* 4.1 24.9 - - - +
484F TRP* 3.7 23.6 - - + +
487F TYR* 3.6 33.9 - - + -
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Residues in contact with ALA 179 (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 VAL* 4.1 16.4 - - + -
175F ASN 2.9 19.3 + - - +
178F ILE* 1.3 75.7 - - - +
180F LEU* 1.3 60.9 + - - +
182F CYS 3.1 7.1 + - - -
184F ASN* 3.0 37.6 + - + +
186F CYS* 3.9 20.4 - - - -
487F TYR* 3.8 20.8 - - + -
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Residues in contact with LEU 180 (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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73F TRP* 3.4 20.0 + - + -
81F ARG* 3.2 16.3 - - - -
84F ILE* 5.4 4.9 - - + -
85F VAL* 3.9 17.0 - - + -
88F ILE* 3.8 16.4 - - + -
176F ASN* 2.9 37.8 + - - +
179F ALA* 1.3 73.6 - - - +
181F THR* 1.3 64.3 + - - +
183F GLY 3.0 11.1 + - - -
184F ASN 3.6 18.2 - - - +
186F CYS* 3.8 16.4 - - - -
209F LEU* 5.7 1.1 - - + -
218F ILE* 3.9 11.4 - - + +
219F CYS* 3.6 28.9 - - - -
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Residues in contact with THR 181 (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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78F ALA* 4.0 3.1 - - - +
81F ARG* 2.6 31.9 + - - -
82F GLY* 4.8 2.0 - - - +
85F VAL* 3.7 10.0 - - - +
128F ALA* 3.2 35.6 + - - +
131F LEU* 4.2 9.2 - - + -
132F SER* 3.6 26.2 - - - +
135F ILE* 3.7 11.9 - - + +
177F ALA 2.7 22.5 + - - -
178F ILE* 3.5 6.5 - - - -
180F LEU* 1.3 77.8 - - - +
182F CYS* 1.3 54.8 + - - +
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Residues in contact with CYS 182 (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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81F ARG* 3.5 4.5 - - - +
135F ILE* 4.2 9.9 - - - -
155F PRO* 3.2 21.7 - - - +
178F ILE* 2.9 25.9 + - - +
179F ALA 3.1 5.5 + - - +
181F THR* 1.3 79.2 - - - +
183F GLY* 1.3 57.4 + - - +
184F ASN* 3.4 13.8 + - - +
484F TRP* 3.8 29.8 - - - -
487F TYR* 4.2 1.8 - - + +
488F MET* 3.4 42.9 - - + +
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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