Contacts of the strand formed by residues 166 - 171 (chain A) in PDB entry 5WN0
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 VAL 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A VAL* 3.7 24.7 - - + -
160A ALA 3.7 8.7 - - - +
161A GLU* 3.9 21.3 - - + +
165A PHE* 1.3 77.4 - - - +
167A LEU* 1.3 57.2 + - - +
199A LEU* 3.6 28.7 - - + +
202A ARG* 6.1 1.3 - - - +
203A LYS* 3.4 28.0 - - + +
204A PRO 2.9 5.8 + - - +
205A LEU* 3.4 15.6 - - + +
206A VAL* 2.8 33.1 + - - +
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Residues in contact with LEU 167 (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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64A ILE* 4.0 15.9 - - + -
91A ILE* 3.6 44.4 - - + -
93A CYS* 4.1 4.7 - - - -
133A LEU* 4.5 12.5 - - + +
158A ILE 3.9 0.9 - - - +
159A VAL* 3.5 2.3 - - - +
160A ALA* 2.7 46.2 + - + +
162A PHE* 4.3 5.8 - - + -
165A PHE* 3.7 13.8 - - + -
166A VAL* 1.3 72.4 - - - +
168A VAL* 1.3 72.8 + - - +
206A VAL* 3.2 29.6 - - + +
208A CYS* 3.8 17.0 - - - -
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Residues in contact with VAL 168 (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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157A VAL* 4.1 19.1 - - + -
158A ILE 3.4 7.4 - - - +
159A VAL* 4.0 22.2 - - + -
166A VAL* 4.7 0.2 - - + -
167A LEU* 1.3 83.5 - - - +
169A THR* 1.3 66.9 + - - +
192A PHE* 4.3 5.8 - - + -
195A PHE* 5.0 1.8 - - + -
196A LEU* 4.0 26.9 - - + -
199A LEU* 5.1 2.0 - - + -
205A LEU* 4.0 17.3 - - + -
206A VAL 2.7 11.7 + - - +
207A LEU* 3.3 21.5 - - + -
208A CYS 3.0 23.7 + - - -
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Residues in contact with THR 169 (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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93A CYS* 3.1 25.7 - - + +
95A GLN* 3.0 27.7 + - - +
131A VAL* 4.6 9.4 - - + -
132A GLY 4.2 10.8 - - - +
133A LEU* 4.3 6.5 - - + +
156A ARG 3.5 0.7 - - - +
157A VAL* 3.2 7.8 - - - +
158A ILE* 3.0 48.2 + - + +
168A VAL* 1.3 77.6 - - - +
170A ALA* 1.3 58.4 + - - +
208A CYS* 3.1 14.0 + - - -
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Residues in contact with ALA 170 (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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95A GLN* 3.3 11.9 - - - +
131A VAL* 4.6 0.4 - - - -
156A ARG 3.2 7.2 - - - +
157A VAL* 4.1 4.5 - - + -
169A THR* 1.3 75.4 - - - +
171A TYR* 1.3 59.4 + - - +
172A VAL* 3.8 17.3 - - + +
188A TRP* 5.2 0.9 - - + -
192A PHE* 3.6 30.7 - - + -
207A LEU* 4.0 7.9 - - + -
208A CYS 3.0 5.7 + - - -
209A GLY* 3.4 0.9 - - - -
210A ASP 3.1 23.5 + - - -
211A LEU* 4.2 4.7 - - + -
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Residues in contact with TYR 171 (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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68A ASN* 3.8 10.5 - - - -
95A GLN* 4.1 6.3 - - + -
96A GLU* 3.0 53.0 + - + -
128A TYR* 6.0 3.0 - + - -
129A SER* 3.6 30.1 - - - -
130A GLY 4.7 0.2 - - - -
131A VAL* 3.7 19.7 - - + -
156A ARG* 2.5 73.5 + - - +
170A ALA* 1.3 72.5 - - - +
172A VAL* 1.3 57.0 + - - +
174A ASN* 5.4 3.0 - - + +
188A TRP* 5.5 0.2 - - - -
210A ASP* 3.7 23.1 - - + -
212A ASN* 3.8 13.3 + - - -
10D C 4.3 17.9 + - - -
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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