Contacts of the strand formed by residues 180 - 186 (chain A) in PDB entry 2W8B
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 TYR 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A VAL* 5.0 7.2 - - + -
171A VAL 3.5 2.9 - - - -
172A GLN* 3.5 45.8 + - + -
178A PHE 3.2 2.1 - - - +
179A PRO* 1.3 90.4 - - + +
181A GLU* 1.3 64.6 + - - +
197A ARG* 3.5 0.5 - - - -
198A SER 2.9 33.2 + - - +
199A PRO 3.3 23.1 - - - -
200A GLN* 3.4 28.9 - - - +
201A PRO* 3.6 32.5 - - + +
202A LEU* 3.8 15.8 - - + +
422A LYS* 6.0 0.4 - - - -
151H GLU 4.6 5.0 + - - -
152H LYS* 4.3 13.9 - - - +
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Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A VAL* 3.2 3.8 - - - +
171A VAL* 2.8 42.9 + - + +
173A THR* 5.9 4.3 - - - +
178A PHE 4.4 11.2 - - - +
179A PRO 5.3 0.9 - - - +
180A TYR* 1.3 78.7 - - - +
182A LEU* 1.3 60.9 + - - +
183A ARG* 2.9 43.9 + - + +
194A VAL* 3.6 12.3 - - + +
196A HIS 3.3 4.3 - - - +
197A ARG* 3.4 41.9 + - + -
202A LEU* 3.9 4.4 - - - +
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A TYR 3.5 18.2 - - - +
170A VAL* 4.0 10.8 - - + +
181A GLU* 1.3 71.9 - - - +
183A ARG* 1.3 63.7 + - - +
194A VAL* 3.8 0.9 - - - +
195A VAL* 2.8 42.6 + - + -
196A HIS* 2.8 20.0 + - + +
202A LEU* 3.5 14.9 - - + +
205A PRO* 3.6 33.2 - - + -
214A LEU* 4.0 15.3 - - + -
216A TYR* 3.5 45.3 - - + -
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Residues in contact with ARG 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLU 5.0 1.2 - - - +
168A ALA* 3.3 4.7 - - - +
169A TYR* 2.8 48.2 + - + -
171A VAL* 3.7 34.6 - - + +
173A THR* 5.2 5.3 - - - +
181A GLU* 2.9 32.7 + - + +
182A LEU* 1.3 80.6 - - - +
184A VAL* 1.3 64.4 + - - +
192A GLN* 3.1 43.7 + - + +
193A PHE 3.3 11.9 - - - +
194A VAL* 4.0 15.7 - - + +
195A VAL* 4.1 2.0 - - - +
418A ASP* 3.0 34.9 + - - +
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Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ARG* 3.7 24.7 - - - -
167A ILE 3.2 9.0 - - - +
168A ALA* 3.9 5.2 - - + -
169A TYR* 4.5 3.1 - - - -
183A ARG* 1.3 78.4 - - - +
185A SER* 1.3 63.3 + - - +
192A GLN* 3.1 4.6 - - - +
193A PHE* 2.8 68.6 + - + -
195A VAL* 3.7 9.4 - - + +
207A TRP* 3.8 17.0 - - + -
214A LEU* 3.7 29.2 - - + -
231A LEU* 4.4 2.5 - - + -
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Residues in contact with SER 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 5.3 0.3 - - - +
166A ARG* 3.1 11.9 - - - +
167A ILE* 2.8 34.3 + - - +
169A TYR* 3.6 27.9 + - - -
184A VAL* 1.3 77.6 - - - +
186A ASP* 1.3 78.8 + - - +
189A GLY* 3.6 26.6 - - - -
190A TYR 3.6 2.2 - - - -
191A ASN 3.8 7.6 - - - -
192A GLN* 3.7 5.6 - - - -
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Residues in contact with ASP 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ARG* 4.6 2.6 + - - +
146A HIS* 4.4 16.4 + - + -
164A ARG 5.6 1.0 - - - +
165A THR 3.7 8.1 - - - +
166A ARG* 4.0 17.6 + - - +
167A ILE* 3.8 2.1 - - - +
185A SER* 1.3 91.5 + - - +
187A TYR* 1.3 68.0 + - - +
188A ASP* 3.1 16.7 - - - +
189A GLY 2.9 6.4 + - - -
190A TYR* 2.9 24.7 + - - +
191A ASN* 2.9 32.8 + - - +
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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