Contacts of the strand formed by residues 165 - 172 (chain E) 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 165 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158E MET* 3.5 3.8 - - - -
159E ARG 2.7 36.4 + - - +
163E ARG* 3.8 17.5 + - - +
164E ALA* 1.3 86.6 + - - +
166E LYS* 1.3 68.5 + - - +
167E VAL* 4.3 1.9 - - - +
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Residues in contact with LYS 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ARG* 3.7 25.9 - - - +
208D SER 5.4 5.6 + - - -
211D ASP* 4.1 0.4 + - - -
156E ASN* 4.4 12.8 - - + +
157E LEU 3.4 7.4 - - - +
158E MET* 3.5 21.9 - - + +
165E GLN* 1.3 79.4 + - - +
167E VAL* 1.3 64.0 + - - +
168E VAL 4.1 1.7 - - - +
169E THR* 3.1 34.7 + - - +
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Residues in contact with VAL 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ILE* 4.9 0.2 - - - +
100D ARG* 3.8 12.6 + - - -
115D ILE* 4.0 35.1 - - + +
157E LEU* 2.7 22.6 + - + +
159E ARG* 3.7 45.3 - - + +
165E GLN 4.3 0.9 - - - +
166E LYS* 1.3 79.2 + - - +
168E VAL* 1.3 67.3 + - + +
185E MET* 4.1 18.4 - - + -
187E LEU* 4.1 13.7 - - + -
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Residues in contact with VAL 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ILE* 3.9 20.4 - - + -
115D ILE* 5.0 0.4 - - + -
211D ASP* 3.3 27.4 - - + +
213D VAL* 4.7 0.9 - - + -
155E VAL 3.9 0.3 - - - +
156E ASN* 3.5 3.6 - - - +
157E LEU* 2.9 38.3 + - + +
166E LYS* 4.1 5.2 - - - +
167E VAL* 1.3 85.7 + - + +
169E THR* 1.3 63.9 + - - +
170E PHE* 3.6 26.2 - - + -
185E MET* 3.6 33.9 - - + -
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Residues in contact with THR 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D GLU 3.6 24.0 - - - +
210D ALA* 3.3 1.8 - - - -
211D ASP* 2.7 43.2 + - - +
154E CYS* 4.5 5.4 - - + -
155E VAL 3.3 8.3 - - - +
156E ASN* 2.8 24.4 + - - +
166E LYS* 3.1 23.0 + - - +
168E VAL* 1.3 72.3 + - - +
170E PHE* 1.3 61.8 + - - +
171E CYS* 4.1 15.3 - - - -
200E THR* 5.3 1.8 - - + -
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Residues in contact with PHE 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D GLN* 4.2 12.3 - - + -
178D VAL* 5.2 10.3 - - + -
210D ALA* 4.7 0.7 - - - -
211D ASP* 4.1 16.6 - - + +
213D VAL* 3.5 33.4 - - + -
145E TYR* 3.1 34.8 + + - +
153E LEU* 3.9 1.0 - - - +
154E CYS* 3.1 1.7 - - - -
155E VAL* 2.7 43.7 + - + +
157E LEU* 5.0 9.0 - - + -
168E VAL* 3.6 22.9 - - + -
169E THR* 1.3 72.8 - - - +
171E CYS* 1.3 60.9 + - - +
181E THR* 5.8 2.0 - - + +
182E THR 4.3 6.5 - - - +
183E GLY* 3.7 27.4 - - - -
184E GLY 3.8 13.5 - - - -
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Residues in contact with CYS 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D LEU* 3.0 28.5 - - - +
176D PHE* 3.7 27.0 - - + +
178D VAL* 3.5 7.5 - - - +
209D GLU* 4.1 6.1 - - - -
210D ALA* 3.8 22.6 - - + +
211D ASP 5.7 0.2 + - - -
153E LEU 3.3 3.4 - - - -
154E CYS* 2.0 46.0 - - - -
169E THR* 4.1 8.1 - - - -
170E PHE* 1.3 74.4 - - - +
172E ASP* 1.3 61.2 + - - +
173E TYR* 4.1 1.8 - - + -
181E THR* 5.3 0.2 - - - -
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Residues in contact with ASP 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D PHE 3.9 2.7 - - - -
177D GLN* 3.4 9.7 - - - -
178D VAL* 3.2 27.3 + - + +
153E LEU* 2.9 22.3 + - - +
170E PHE 4.4 0.2 - - - -
171E CYS* 1.3 74.0 - - - +
173E TYR* 1.3 63.9 + - - +
179E GLN* 3.0 28.6 + - - +
180E VAL 4.6 2.4 - - - +
181E THR* 2.7 44.3 + - + +
1224E CA 2.3 27.2 - - - -
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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