Contacts of the strand formed by residues 179 - 185 (chain D) in PDB entry 3WBR
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 ARG 179 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145D SER* 3.2 6.4 - - - -
146D ASP* 2.8 32.4 + - + +
177D ASP* 3.9 0.8 + - - -
178D GLU* 1.3 77.6 - - - +
180D CYS* 1.3 60.2 + - - +
195D ASP* 3.1 36.4 + - + +
196D ILE* 3.5 17.5 + - - +
197D HIS* 3.3 26.4 - - - +
198D CYS* 3.4 4.9 - - - -
151E ARG* 3.1 46.0 - - - +
153E TRP* 3.8 17.3 - - + -
174E ASN* 3.4 18.4 + - - +
197F HIS* 6.3 1.6 - - - -
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Residues in contact with CYS 180 (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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104D TRP* 3.3 41.1 - - + -
141D PHE* 3.9 12.8 - - + -
144D LEU 3.7 4.3 - - - -
145D SER* 3.9 7.0 - - - +
179D ARG* 1.3 76.8 - - - +
181D ALA* 1.3 61.9 + - - +
195D ASP* 3.4 1.4 - - - -
196D ILE* 2.9 39.4 + - - +
198D CYS* 2.0 46.0 - - - -
153E TRP* 4.2 4.7 - - - -
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Residues in contact with ALA 181 (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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141D PHE* 3.6 10.0 - - - -
142D LEU* 3.0 35.4 + - + +
144D LEU* 2.9 35.9 + - + +
180D CYS* 1.3 73.9 - - - +
182D ILE* 1.3 60.6 + - - +
193D TRP* 5.1 0.2 - - + -
194D ASN 3.2 5.8 - - - +
195D ASP* 4.5 0.9 - - - +
153E TRP* 4.2 1.5 - - + -
168E TRP* 3.8 28.0 - - + -
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Residues in contact with ILE 182 (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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139D SER* 3.5 10.8 - - - +
140D TYR 3.1 11.7 - - - +
141D PHE* 3.6 26.9 - - + -
142D LEU* 4.2 5.2 - - - +
181D ALA* 1.3 71.5 - - - +
183D ILE* 1.3 60.3 + - - +
184D ASN* 3.3 26.9 + - - +
193D TRP* 3.0 7.1 - - - +
194D ASN* 2.7 50.7 + - + +
196D ILE* 3.7 33.9 - - + -
202D GLN* 3.6 22.2 - - - +
201F PRO* 4.2 7.0 - - + -
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Residues in contact with ILE 183 (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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121D ILE* 4.8 3.1 - - + -
127D GLN* 3.6 34.1 - - - +
130D ILE* 4.8 3.8 - - + -
131D ILE* 4.0 18.4 - - + -
134D LEU* 4.2 11.0 - - + -
139D SER* 3.6 1.2 - - - -
140D TYR* 2.7 44.6 + - + +
142D LEU* 3.6 26.9 - - + +
182D ILE* 1.3 74.1 - - - +
184D ASN* 1.3 65.5 + - - +
191D TRP* 4.2 9.4 - - + -
192D GLY 3.3 13.5 - - - +
193D TRP* 4.1 7.9 - - + +
205D ILE* 3.8 18.8 - - + -
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Residues in contact with ASN 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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138D SER 3.8 5.4 - - - +
139D SER* 3.2 29.4 + - - +
182D ILE* 3.3 23.2 - - - +
183D ILE* 1.3 75.9 - - - +
185D PHE* 1.3 62.0 + - - +
186D ARG* 4.3 9.2 + - - +
191D TRP* 3.4 14.9 - - - -
192D GLY 3.0 18.3 + - - -
194D ASN* 4.7 7.2 + - - +
169E HIS* 3.0 38.4 + - - -
201F PRO* 4.0 14.1 - - + +
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Residues in contact with PHE 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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136D ARG* 3.6 69.6 + - + +
138D SER 4.5 2.0 + - - -
184D ASN* 1.3 77.0 - - - +
186D ARG* 1.3 83.9 + - - +
187D SER* 4.0 13.7 - - - -
190D GLU* 3.4 39.7 - - + -
191D TRP* 3.4 38.0 - + + -
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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