Contacts of the strand formed by residues 208 - 216 (chain C) 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 VAL 208 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU* 4.0 19.1 - - + -
167A PHE* 3.8 10.1 - - + -
182A GLY 3.5 23.6 - - - +
95C THR* 3.2 33.7 - - + -
96C VAL 3.3 7.9 - - - +
112C PHE* 3.9 4.9 - - - -
116C LEU* 4.9 0.4 - - + -
141C VAL 5.8 0.2 - - - +
142C TYR* 3.2 7.5 - - - +
143C HIS* 2.8 59.7 + - + +
144C ALA* 5.6 0.3 - - - +
207C SER* 1.3 74.6 - - - +
209C PHE* 1.3 63.0 + - - +
210C SER* 4.2 4.5 - - - +
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Residues in contact with PHE 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C PHE* 3.5 18.1 - + - -
95C THR* 3.5 0.5 - - - -
96C VAL* 3.0 33.4 + - + -
112C PHE* 3.8 22.4 - + + -
123C TYR* 3.8 30.7 - + - -
130C PHE* 5.4 0.9 - - + -
140C PHE* 4.1 29.4 - + + -
141C VAL 3.5 11.2 - - - -
142C TYR* 4.0 2.0 - + + -
154C LEU* 4.6 1.6 - - + -
189C VAL* 4.4 13.5 - - + -
190C TRP* 4.7 5.6 - - - -
191C LEU* 3.8 47.8 - - + -
208C VAL* 1.3 75.1 - - - +
210C SER* 1.3 77.2 + - - +
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Residues in contact with SER 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A TYR* 4.1 17.2 + - - -
182A GLY 4.5 1.0 + - - -
183A MET* 4.2 1.7 - - - -
184A VAL* 4.6 3.4 - - - -
94C PHE* 3.4 15.5 - - - -
95C THR* 2.8 25.7 + - - +
140C PHE* 3.3 2.6 - - - -
141C VAL* 2.7 56.9 + - - +
208C VAL* 4.2 5.6 - - - +
209C PHE* 1.3 78.4 - - - +
211C GLY* 1.3 57.3 + - - +
212C PHE* 5.1 2.5 - - - -
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Residues in contact with GLY 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C VAL* 3.4 1.9 - - - -
94C PHE* 3.0 51.1 + - - +
130C PHE* 6.1 0.2 - - - -
138C TYR* 5.0 1.8 - - - -
139C TYR 3.0 12.1 - - - -
140C PHE* 3.8 9.6 - - - -
210C SER* 1.3 76.9 - - - +
212C PHE* 1.3 65.4 + - - +
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Residues in contact with PHE 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A TYR* 3.8 28.9 - + + -
184A VAL* 4.1 8.3 - - + -
217A PHE* 3.9 29.2 - + - -
219A ILE* 3.6 32.1 - - + -
218B PHE* 4.6 1.3 - + - -
92C SER 3.3 11.7 - - - +
93C VAL* 3.5 12.1 - - + -
138C TYR* 3.3 10.8 - - - -
139C TYR* 2.8 68.0 + + + -
141C VAL* 5.3 0.9 - - + -
210C SER* 5.1 3.1 - - - -
211C GLY* 1.3 80.2 - - - +
213C LEU* 1.3 62.4 + - - +
214C LEU* 3.5 25.4 + - + +
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Residues in contact with LEU 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ILE* 4.3 15.8 - - - +
220A PHE* 5.5 0.3 - - - -
90C PHE 4.1 10.3 - - - +
91C GLN* 4.4 12.4 - - - +
92C SER* 2.8 25.5 + - - +
134C VAL* 3.5 34.8 - - + +
136C GLY* 4.0 5.4 - - - -
137C LEU 3.5 19.7 - - - +
138C TYR* 3.6 33.9 - - + -
212C PHE* 1.3 70.4 - - - +
214C LEU* 1.3 61.1 + - - +
215C PHE 3.8 17.5 - - - +
216C PRO* 3.9 21.3 - - + -
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Residues in contact with LEU 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A PHE* 5.3 1.3 - - + -
219A ILE* 5.1 6.7 - - + +
91B ALA* 4.9 0.7 + - - +
218B PHE* 3.5 44.6 - - + -
219B LEU 5.2 3.4 - - - +
220B LEU* 5.3 4.7 - - + -
137C LEU* 2.7 19.7 + - + +
139C TYR* 4.0 9.2 - - + +
180C LEU* 3.7 21.5 - - + -
212C PHE* 3.5 29.6 + - + +
213C LEU* 1.3 78.1 - - - +
215C PHE* 1.3 82.8 + - + +
216C PRO* 3.7 8.2 - - - +
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Residues in contact with PHE 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ALA* 3.9 17.3 - - + +
93B GLN 5.0 3.1 - - - -
94B LYS* 3.8 32.5 - - + -
95B ILE 3.5 36.6 - - - -
96B ALA* 3.7 3.4 - - + -
122B MET* 4.8 2.4 - - + +
218B PHE* 4.5 1.8 - - + -
219B LEU* 3.5 32.1 - - + -
220B LEU 5.7 1.3 - - - -
136C GLY* 3.2 2.1 - - - -
137C LEU* 2.8 67.0 + - + -
213C LEU* 3.9 2.2 - - - -
214C LEU* 1.3 91.7 - - + +
216C PRO* 1.3 67.2 - - - +
217C ASP* 4.3 2.1 - - - +
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Residues in contact with PRO 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ALA* 3.8 19.1 + - + +
94B LYS* 2.9 21.8 + - - -
90C PHE 4.9 6.3 - - - +
91C GLN* 5.5 7.6 - - - +
134C VAL* 4.7 5.4 - - + -
135C PRO 3.7 8.5 - - - +
213C LEU* 3.9 22.9 - - + -
214C LEU 3.7 9.6 - - - +
215C PHE* 1.3 84.6 - - - +
217C ASP* 1.3 66.5 + - - +
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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