Contacts of the strand formed by residues 183 - 192 (chain D) in PDB entry 4JRY
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 PHE 183 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153D ASP* 4.6 9.6 - - - -
176D LEU* 4.8 0.4 - - + -
177D ASP* 3.3 3.4 + - - +
178D MET* 2.7 58.6 + - + -
181D MET* 4.0 18.6 - - + +
182D ASP* 1.3 77.7 - - - +
184D LYS* 1.3 67.9 + - - +
185D SER* 3.7 22.2 - - - -
152E LYS* 3.7 28.0 - - + +
207E ARG* 3.5 29.6 - - - -
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Residues in contact with LYS 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLU* 3.3 35.4 + - - +
95D VAL* 6.5 0.9 - - - -
96D HIS* 5.1 9.4 - - + +
97D ASP* 6.2 0.2 - - - -
126D PRO* 4.0 23.1 - - + -
128D ILE* 3.7 17.5 - - + +
175D VAL* 4.6 8.7 - - + -
176D LEU 3.3 5.8 - - - +
177D ASP* 3.5 39.6 + - + +
182D ASP* 4.5 8.3 + - - -
183D PHE* 1.3 83.8 - - - +
185D SER* 1.3 61.9 + - - +
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Residues in contact with SER 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ILE* 4.2 6.5 - - - -
152D THR* 4.3 5.2 + - - -
153D ASP* 4.1 11.4 - - - +
174D CYS 3.6 0.7 - - - +
175D VAL* 3.3 6.4 - - - +
176D LEU* 2.9 51.3 + - - +
183D PHE* 3.7 18.8 - - - -
184D LYS* 1.3 75.0 - - - +
186D ASN* 1.3 65.0 + - - +
187D SER* 5.3 0.9 + - - -
207E ARG* 3.4 20.0 + - - -
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Residues in contact with ASN 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PRO* 3.7 6.9 - - - +
128D ILE* 3.4 14.5 - - - +
151D PHE 3.9 0.2 - - - +
152D THR* 3.2 6.9 + - - -
153D ASP* 3.1 26.3 + - - +
154D PHE* 3.1 47.4 + - + +
155D ASP 4.0 0.2 - - - -
156D SER* 3.3 28.2 + - - +
173D LYS* 4.5 13.3 - - + +
174D CYS 3.2 5.9 - - - +
175D VAL* 3.3 26.7 - - - +
185D SER* 1.3 75.8 - - - +
187D SER* 1.3 61.3 + - - +
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Residues in contact with SER 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D LEU* 3.7 23.1 - - - -
151D PHE 3.1 6.7 - - - -
152D THR* 4.1 7.0 - - - -
154D PHE* 4.4 2.5 - - - -
173D LYS* 3.2 3.3 - - - -
174D CYS* 2.8 34.8 + - - +
176D LEU* 4.7 10.4 - - - +
185D SER* 5.5 1.1 - - - -
186D ASN* 1.3 76.6 - - - +
188D ALA* 1.3 60.0 + - - +
154E THR* 5.9 1.1 - - - -
183E CYS* 5.1 0.3 - - - +
205E ARG* 3.0 36.8 + - - +
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Residues in contact with ALA 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D LEU* 3.6 3.6 - - - +
151D PHE* 2.8 37.9 + - + +
154D PHE* 4.6 0.4 - - + -
160D VAL* 3.7 41.1 - - + -
171D THR* 3.8 8.1 - - - +
172D ASP 4.2 0.2 - - - -
173D LYS* 4.5 1.3 - - - -
187D SER* 1.3 74.1 - - - +
189D VAL* 1.3 65.3 + - - +
203D PHE* 3.8 11.6 - - + -
205E ARG* 3.8 4.3 - - - +
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Residues in contact with VAL 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D VAL* 3.9 21.1 - - + -
149D CYS 3.6 9.0 - - - +
150D LEU* 4.0 13.7 - - + -
169D TYR 3.7 0.7 - - - +
170D ILE* 3.3 3.1 - - - +
171D THR* 2.8 45.7 + - + +
188D ALA* 1.3 79.9 - - - +
190D ALA* 1.3 63.2 + - - +
191D TRP* 4.1 18.1 - - + -
203D PHE* 4.2 2.0 - - - -
156E VAL* 3.9 22.7 - - + -
158E LEU* 4.5 2.0 - - + -
203E SER* 4.2 6.5 - - - +
205E ARG* 3.7 27.8 - - + +
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Residues in contact with ALA 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D VAL* 3.6 2.1 - - - +
149D CYS* 2.7 40.8 + - + +
168D VAL* 5.2 0.2 - - + -
169D TYR 3.1 8.7 - - - +
170D ILE* 3.8 13.5 - - + -
189D VAL* 1.3 73.3 - - - +
191D TRP* 1.3 65.4 + - - +
197D PHE* 4.3 6.7 - - + -
202D ALA* 4.1 16.2 - - + -
203D PHE* 3.6 25.7 - - + -
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Residues in contact with TRP 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LYS* 3.5 29.6 - - + +
147D SER 3.8 14.8 - - - +
148D VAL* 3.9 9.9 - - + -
168D VAL* 3.7 0.5 - - - -
169D TYR* 2.9 66.3 + + + -
171D THR* 3.5 26.7 - - + -
189D VAL* 4.1 10.8 - - + -
190D ALA* 1.3 81.4 - - - +
192D SER* 1.3 63.6 + - - +
193D ASN* 5.0 3.3 - - - +
197D PHE* 4.3 5.8 - - - -
158E LEU* 3.6 38.9 - - + +
160E THR* 4.5 8.3 - - + +
189E LEU* 3.6 18.2 - - + -
201E ALA* 3.5 28.9 - - + +
202E LEU 4.9 2.9 - - - -
203E SER* 4.7 1.6 - - - -
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Residues in contact with SER 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LYS* 2.9 26.6 - - - +
147D SER 4.1 2.1 + - - -
167D ASP 2.6 27.2 + - - -
168D VAL* 3.4 8.0 - - - +
191D TRP* 1.3 80.0 - - - +
193D ASN* 1.3 59.4 + - - +
194D LYS* 3.6 21.7 + - - +
197D PHE* 3.5 38.6 - - - +
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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