Contacts of the strand formed by residues 173 - 183 (chain F) in PDB entry 2JG8
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 173 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168D CYS 3.9 3.1 - - - -
169D ASP* 3.2 21.9 + - - +
171D THR* 3.2 23.5 + - - +
177D GLN* 3.4 16.2 + - - -
178E PHE 5.4 0.7 - - - +
179E GLN* 5.8 4.8 - - - +
1224E CA 4.1 6.1 - - - -
145F SER* 3.4 4.7 - - - -
146F HIS* 3.2 45.9 + - + +
166F GLY* 5.6 0.7 - - - -
167F HIS 3.3 24.4 + - - +
168F THR* 3.7 14.5 - - - +
171F THR 3.9 0.8 + - - -
172F ASN* 1.3 81.4 + - - +
174F VAL* 1.3 65.7 + - - +
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Residues in contact with VAL 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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167D PHE* 4.3 4.0 - - + -
168D CYS 3.5 28.5 + - - +
169D ASP* 4.9 2.2 + - - +
178D VAL 5.2 5.9 + - - +
179D VAL* 4.2 8.3 - - + +
180D SER* 3.6 43.3 + - - +
180E VAL* 4.2 12.3 - - - +
143F HIS* 4.0 8.5 - - + -
144F ALA 3.5 14.8 - - - +
145F SER* 3.9 13.7 - - - +
146F HIS* 4.2 2.7 - - - -
173F GLN* 1.3 79.2 - - - +
175F ASN* 1.3 71.6 + - - +
176F SER* 3.8 3.3 + - - -
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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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180E VAL* 3.8 14.5 - - + +
142F TYR* 2.7 31.1 + - + -
143F HIS* 3.5 0.9 - - - -
144F ALA 2.6 45.8 + - - +
146F HIS* 3.8 17.8 - - + +
150F LEU* 3.2 28.6 + - + -
152F VAL* 4.0 7.5 - - - +
164F PHE* 2.9 27.8 + - - +
166F GLY 3.7 4.0 - - - +
174F VAL* 1.3 70.8 - - - +
176F SER* 1.3 64.0 + - - +
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Residues in contact with SER 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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180D SER* 3.8 9.0 - - - -
146E HIS* 3.1 18.5 + - - -
180E VAL* 3.5 24.1 + - - +
181E THR 4.6 2.4 + - - -
182E THR* 3.4 17.5 - - - +
142F TYR* 3.3 19.4 + - - -
143F HIS* 3.7 21.8 - - - -
164F PHE* 3.8 2.1 - - - +
174F VAL 3.8 3.4 + - - -
175F ASN* 1.3 81.1 + - - +
177F GLY* 1.3 59.7 + - - +
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Residues in contact with GLY 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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146E HIS* 3.4 14.2 - - - -
141F VAL* 3.3 4.7 - - - +
142F TYR* 2.9 51.6 + - - -
164F PHE* 3.6 13.2 - - - -
176F SER* 1.3 77.8 - - - +
178F GLY* 1.3 58.6 + - - -
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Residues in contact with GLY 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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146E HIS* 3.4 13.8 + - - -
214E ILE* 3.5 23.6 - - - +
216E SER* 4.8 1.9 + - - -
139F TYR* 4.6 4.7 - - - -
140F PHE 3.1 13.9 - - - -
141F VAL* 4.0 3.8 - - - -
142F TYR* 4.5 0.2 - - - -
154F LEU* 6.0 2.0 - - - -
162F VAL* 4.7 2.5 - - - +
164F PHE* 3.9 8.8 - - - -
177F GLY* 1.3 75.2 - - - -
179F VAL* 1.3 68.2 + - - +
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Residues in contact with VAL 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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98E SER* 3.9 10.1 - - - +
119E ILE* 4.1 15.5 - - + -
214E ILE* 3.9 19.3 - - + -
216E SER* 4.6 2.9 - - - -
138F TYR 3.9 0.5 - - - +
139F TYR* 3.6 6.3 - - - -
140F PHE* 3.0 31.4 + - + +
154F LEU* 4.1 30.1 - - + -
161F VAL* 4.3 3.6 - - + -
162F VAL* 4.4 9.9 - - + -
178F GLY* 1.3 76.6 - - - +
180F LEU* 1.3 74.9 + - - +
181F LEU* 4.1 23.9 + - + -
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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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96E ALA* 3.8 6.3 - - + -
97E PHE 3.3 30.7 - - - +
98E SER* 2.9 15.1 + - - +
120E THR* 2.7 28.3 + - - +
216E SER* 4.2 4.0 - - - -
217E GLY 3.6 20.2 - - - +
218E PHE* 3.9 11.4 - - + -
137F LEU* 4.0 14.8 - - + -
138F TYR 3.2 6.1 - - - +
139F TYR* 3.4 37.0 - - + -
179F VAL* 1.3 79.6 - - - +
181F LEU* 1.3 64.0 + - - +
214F LEU* 3.9 16.8 - - + -
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Residues in contact with LEU 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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119E ILE* 3.9 22.2 - - + -
120E THR* 4.1 2.7 - - - +
136F GLY 3.6 0.2 - - - +
137F LEU* 4.0 3.6 - - - +
138F TYR* 2.8 37.3 + - - +
140F PHE* 4.1 21.8 - - + -
154F LEU* 4.1 26.5 - - + -
156F ARG* 4.1 38.6 - - + +
161F VAL* 4.3 8.3 - - + -
179F VAL* 4.1 13.6 + - + -
180F LEU* 1.3 82.4 - - - +
182F ARG* 1.3 58.7 + - - +
183F LEU* 3.5 17.6 + - + +
189F VAL* 4.6 2.0 - - + -
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Residues in contact with ARG 182 (chain F).
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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94E LYS* 4.7 8.5 - - - +
120E THR* 4.5 8.5 + - + -
122E MET* 3.8 38.3 - - - +
136F GLY 3.4 10.1 - - - +
137F LEU* 4.0 13.8 - - + +
156F ARG* 3.1 22.2 + - - +
181F LEU* 1.3 68.9 - - - +
183F LEU* 1.3 63.2 + - - +
184F GLN* 4.2 3.5 + - - +
217F ASP* 3.0 37.3 + - - +
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Residues in contact with LEU 183 (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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130F PHE* 3.7 29.8 - - + -
132F CYS* 4.1 14.8 - - + -
135F PRO* 3.4 5.0 - - - +
136F GLY* 2.8 35.9 + - - +
138F TYR* 3.9 10.1 - - + -
140F PHE* 3.7 17.7 - - + -
156F ARG* 3.6 35.0 - - + +
181F LEU* 3.8 29.6 - - + +
182F ARG* 1.3 74.1 - - - +
184F GLN* 1.3 62.7 + - - +
187F GLU* 3.5 10.5 - - + +
189F VAL* 4.1 7.4 - - + -
217F ASP* 4.4 1.2 - - - +
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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