Contacts of the strand formed by residues 207 - 216 (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 SER 207 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97F THR* 2.8 25.0 + - - -
98F ARG* 3.1 25.9 + - - -
112F PHE* 3.9 3.1 - - - -
143F HIS 3.3 4.0 - - - -
144F ALA* 3.4 5.6 - - - -
145F SER* 2.9 28.9 + - - -
199F MET* 3.4 33.6 + - - +
206F ASP* 1.3 74.8 + - - +
208F VAL* 1.3 59.9 + - - +
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Residues in contact with VAL 208 (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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165D LEU* 3.8 25.8 - - + -
167D PHE* 4.0 7.9 - - + -
182D GLY 3.4 23.8 - - - +
183D MET* 4.9 0.2 - - + -
95F THR* 3.3 26.9 - - + -
96F VAL 3.2 18.2 - - - +
112F PHE* 4.0 5.1 - - - -
116F LEU* 4.5 0.7 - - + -
141F VAL 5.7 0.2 - - - +
142F TYR* 3.2 7.3 - - - +
143F HIS* 2.8 55.3 + - + +
144F ALA* 4.8 0.7 - - - +
207F SER* 1.3 75.3 - - - +
209F PHE* 1.3 58.8 + - - +
210F SER* 4.9 2.7 - - - +
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Residues in contact with PHE 209 (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 PHE* 3.5 19.3 - + - -
95F THR* 3.4 0.9 - - - -
96F VAL* 2.8 44.1 + - + +
112F PHE* 3.9 22.4 - + + -
123F TYR* 3.9 30.5 - + - -
130F PHE* 5.4 0.7 - - + -
140F PHE* 4.2 22.9 - + + -
141F VAL 3.4 11.4 - - - -
142F TYR* 4.1 1.1 - + + -
154F LEU* 4.6 0.7 - - + -
189F VAL* 4.4 14.1 - - + -
190F TRP* 4.8 4.3 - - - -
191F LEU* 3.7 47.3 - - + -
208F VAL* 1.3 74.5 - - - +
210F SER* 1.3 75.4 + - - +
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Residues in contact with SER 210 (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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138D TYR* 4.0 25.0 + - - -
182D GLY 4.5 3.3 + - - -
183D MET* 4.1 3.1 - - - -
184D VAL* 4.5 3.1 - - - -
94F PHE* 3.3 11.2 - - - -
95F THR* 2.6 31.2 + - - +
140F PHE* 3.5 2.6 - - - -
141F VAL* 2.9 41.6 + - - +
208F VAL* 4.3 2.8 - - - +
209F PHE* 1.3 79.1 - - - +
211F GLY* 1.3 58.6 + - - +
212F PHE* 5.0 1.6 - - - -
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Residues in contact with GLY 211 (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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92F SER 5.3 0.2 - - - -
93F VAL* 3.3 1.7 - - - -
94F PHE* 2.9 53.2 + - - +
130F PHE* 6.1 0.2 - - - -
138F TYR* 5.1 2.0 - - - -
139F TYR 3.0 13.0 - - - -
140F PHE* 4.0 7.0 - - - -
210F SER* 1.3 76.0 - - - +
212F PHE* 1.3 66.1 + - - +
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Residues in contact with PHE 212 (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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138D TYR* 3.8 30.5 - + + -
184D VAL* 4.0 7.4 - - + -
217D PHE* 4.0 29.2 - + - -
219D ILE* 3.8 27.4 - - + -
218E PHE* 4.6 1.1 - + - -
92F SER 3.2 12.3 - - - +
93F VAL* 3.7 11.4 - - + -
138F TYR* 3.4 9.6 - - - -
139F TYR* 3.0 65.3 + + + -
141F VAL* 5.1 0.9 - - + -
210F SER* 5.0 1.8 - - - -
211F GLY* 1.3 81.6 - - - +
213F LEU* 1.3 63.5 + - - +
214F LEU* 3.6 27.3 + - + +
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Residues in contact with LEU 213 (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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219D ILE* 4.4 14.0 - - - +
220D PHE* 5.8 0.3 - - - -
90F PHE 4.0 13.9 - - - +
91F GLN* 4.3 17.8 - - - +
92F SER* 2.8 19.9 + - - +
134F VAL* 3.7 34.1 - - + -
135F PRO 4.3 0.4 - - - +
136F GLY* 4.0 4.5 - - - -
137F LEU 3.4 20.9 - - - +
138F TYR* 3.6 33.0 - - + +
212F PHE* 1.3 71.4 - - - +
214F LEU* 1.3 65.3 + - - +
215F PHE 3.7 20.2 - - - +
216F PRO* 3.9 16.2 - - + -
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Residues in contact with LEU 214 (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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217D PHE* 5.2 1.3 - - + -
219D ILE* 5.4 6.7 - - + +
218E PHE* 3.5 48.7 - - + -
219E LEU 5.3 2.2 - - - +
220E LEU* 4.9 5.8 - - + -
137F LEU* 2.8 25.2 + - + +
139F TYR* 4.0 10.5 - - + +
180F LEU* 3.9 21.8 - - + -
212F PHE* 3.9 24.5 - - + +
213F LEU* 1.3 76.8 - - - +
215F PHE* 1.3 77.4 + - + +
216F PRO* 4.0 6.9 - - - +
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Residues in contact with PHE 215 (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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93E GLN 4.4 5.8 - - - -
94E LYS* 3.8 41.6 + - + +
95E ILE 3.5 35.2 - - - -
96E ALA* 4.0 0.9 - - + -
122E MET* 4.8 1.5 - - + +
218E PHE* 4.7 2.0 - - + -
219E LEU* 3.3 34.5 - - + -
220E LEU 5.6 1.6 - - - -
136F GLY* 3.2 1.0 - - - -
137F LEU* 2.9 63.6 + - + -
213F LEU* 3.7 3.4 - - - -
214F LEU* 1.3 100.6 - - + +
216F PRO* 1.3 69.0 - - + +
217F ASP* 4.8 0.9 - - - +
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Residues in contact with PRO 216 (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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94E LYS* 2.5 30.4 + - - -
90F PHE 4.8 6.7 - - - +
91F GLN* 5.7 5.6 - - - +
134F VAL* 4.7 7.0 - - + -
135F PRO 3.7 9.0 - - - +
213F LEU* 3.9 21.3 - - + -
214F LEU 4.0 6.1 - - - +
215F PHE* 1.3 86.2 - - + +
217F ASP* 1.3 59.1 + - - +
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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
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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