Contacts of the strand formed by residues 185 - 195 (chain D) in PDB entry 5WJ9
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 ASP 185 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A VAL* 3.8 19.1 - - + +
290A PHE* 5.4 2.5 - - + -
170D TYR* 4.2 8.7 - - - -
171D HIS* 4.5 1.3 + - - +
172D ARG* 3.2 37.1 + - + +
183D ASP* 6.0 0.2 - - - +
184D ILE* 1.3 79.3 - - - +
186D PRO* 1.3 69.2 - - + +
187D MET* 2.8 37.3 + - - +
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Residues in contact with PRO 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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245A LEU* 4.2 32.7 - - + +
248A ASN* 5.2 5.8 - - - +
250A ILE* 5.9 0.4 - - + -
289A VAL* 5.9 1.1 - - + -
290A PHE* 4.7 28.0 - - + -
170D TYR* 4.3 15.7 - - + -
184D ILE 4.8 0.4 - - - +
185D ASP* 1.3 81.4 - - + +
187D MET* 1.3 58.7 + - - +
188D VAL* 4.0 5.7 + - + +
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Residues in contact with MET 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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170D TYR* 3.7 2.6 - - - -
171D HIS* 2.8 61.3 + - + +
185D ASP* 2.8 26.9 + - - +
186D PRO* 1.3 72.8 - - - +
188D VAL* 1.3 66.1 + - - +
189D VAL* 5.5 1.3 - - + -
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Residues in contact with VAL 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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168D ARG* 4.5 30.3 - - + +
169D TYR 3.5 7.0 - - - +
170D TYR* 5.2 5.2 - - + -
186D PRO* 4.3 3.3 + - + -
187D MET* 1.3 76.2 - - - +
189D VAL* 1.3 61.9 + - - +
190D THR* 3.8 10.9 + - - +
229D VAL* 4.2 27.4 - - + -
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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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167D GLN 2.9 15.1 - - - +
168D ARG* 3.8 1.5 - - - -
169D TYR* 2.8 56.0 + - + +
171D HIS* 3.6 47.8 - - + +
187D MET* 5.0 1.8 - - + -
188D VAL* 1.3 72.9 - - - +
190D THR* 1.3 64.1 + - - +
191D ASP* 4.6 0.9 - - - +
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Residues in contact with THR 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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166D CYS* 4.0 11.0 - - + -
167D GLN 3.5 4.3 - - - +
168D ARG* 5.0 11.7 - - + +
188D VAL* 3.8 13.9 + - - +
189D VAL* 1.3 76.6 - - - +
191D ASP* 1.3 58.3 + - - +
192D CYS* 3.2 32.9 + - - +
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Residues in contact with ASP 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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165D LEU 3.7 1.9 - - - +
166D CYS* 3.3 1.4 - - - -
167D GLN* 2.8 59.4 + - + +
169D TYR* 3.8 23.5 - - + +
189D VAL* 3.6 3.1 + - + +
190D THR* 1.3 69.0 - - - +
192D CYS* 1.3 58.4 + - - +
193D ILE* 3.5 27.1 + - - +
221D LEU* 4.4 1.7 - - - +
222D THR 5.1 1.2 - - - +
224D LYS* 6.2 0.2 - - - -
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Residues in contact with CYS 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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156D PRO* 4.6 7.6 - - - -
165D LEU 3.4 3.6 - - - -
166D CYS* 2.0 46.0 - - - -
190D THR* 3.2 25.1 + - - +
191D ASP* 1.3 73.1 + - - +
193D ILE* 1.3 66.9 + - - +
194D GLN* 3.0 31.0 - - - +
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Residues in contact with ILE 193 (chain D).
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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163D LEU 3.9 0.7 - - - +
164D ALA* 3.5 2.3 - - - -
165D LEU* 2.8 44.0 + - + +
191D ASP* 3.5 30.3 - - - +
192D CYS* 1.3 74.6 - - - +
194D GLN* 1.3 67.6 + - - +
195D VAL* 3.9 5.2 + - + +
217D SER* 4.6 10.3 - - - +
218D TYR* 4.2 31.2 - - + +
221D LEU* 3.8 26.2 - - + -
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Residues in contact with GLN 194 (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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156D PRO 3.0 26.9 + - - -
157D TRP* 4.3 2.0 - - - +
158D THR* 3.6 27.9 - - + +
161D SER* 3.3 31.0 - - - +
163D LEU 3.7 3.1 - - - -
164D ALA* 3.8 6.6 - - + +
192D CYS* 3.0 32.8 - - - +
193D ILE* 1.3 79.7 - - - +
195D VAL* 1.3 63.7 + - - +
217D SER* 5.5 4.7 - - - -
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Residues in contact with VAL 195 (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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133D VAL* 4.6 9.0 - - + -
136D TYR* 4.1 1.3 - - - -
137D LEU* 4.3 18.8 - - + -
161D SER* 4.3 1.9 - - - -
162D GLY 4.1 2.0 - - - -
163D LEU* 2.8 73.5 + - + +
165D LEU* 6.1 2.2 - - + +
193D ILE* 4.6 5.4 - - + +
194D GLN* 1.3 77.3 - - - +
196D ASP* 1.3 65.8 + - - +
216D SER* 5.0 9.6 - - - +
217D SER* 6.5 0.4 - - - -
218D TYR* 4.6 22.7 - - + -
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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