Contacts of the strand formed by residues 168 - 173 (chain A) in PDB entry 3HAD
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 LEU 168 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A PHE* 4.4 6.4 - - - -
160A PHE* 3.7 29.6 + - + -
166A MET* 3.4 7.0 - - + +
167A LYS* 1.3 81.3 - - - +
169A VAL* 1.3 65.7 + - - +
170A GLU* 4.3 5.2 - - + -
194A LYS* 4.9 2.1 - - - +
195A HIS 3.3 18.2 - - - +
197A VAL* 3.7 26.9 - - + -
207A VAL* 3.5 23.1 - - + -
234B THR* 4.3 9.9 - - + +
235B ALA* 3.5 33.2 - - + +
238B LEU* 3.8 17.8 + - + +
239B GLY* 3.8 9.2 - - - +
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Residues in contact with VAL 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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157A LEU* 3.7 32.1 - - + -
158A HIS 3.3 16.6 - - - +
159A PHE* 4.0 23.6 - - + -
168A LEU* 1.3 77.9 - - - +
170A GLU* 1.3 64.1 + - - +
171A VAL* 3.8 0.4 + - + -
189A SER* 3.3 32.5 - - - +
194A LYS* 4.0 12.1 - - + -
195A HIS 3.3 2.7 + - - +
196A PRO* 3.2 12.4 - - + +
197A VAL* 3.0 22.5 + - - +
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Residues in contact with GLU 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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156A GLY 3.7 0.2 - - - +
157A LEU* 3.6 2.1 - - - -
158A HIS* 2.5 71.2 + - + +
160A PHE* 3.3 23.6 - - + -
168A LEU* 4.3 3.4 - - + -
169A VAL* 1.3 72.6 - - - +
171A VAL* 1.3 62.6 + - - +
172A ILE* 3.6 17.0 + - + +
197A VAL* 3.6 20.9 - - + +
199A CYS* 5.2 2.2 - - + +
204A GLY 4.6 0.9 - - - +
205A PHE* 3.6 11.7 - - - +
206A ILE* 2.8 34.0 + - - +
207A VAL* 3.0 13.7 + - - +
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Residues in contact with VAL 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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155A ALA* 5.6 0.7 - - + -
156A GLY 3.6 3.6 - - - -
157A LEU* 4.1 8.5 - - + -
169A VAL* 4.4 1.1 - - + +
170A GLU* 1.3 71.5 - - - +
172A ILE* 1.3 64.1 + - - +
173A LYS 3.8 1.4 + - - -
182A PHE* 3.6 36.2 - - + +
185A LEU* 4.1 29.4 - - + +
186A VAL* 4.5 8.3 - - + -
189A SER* 3.8 13.2 - - - +
196A PRO* 3.7 29.4 - - + -
197A VAL 2.8 14.8 + - - +
198A SER* 3.7 2.9 + - - -
199A CYS 3.4 19.2 + - - -
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Residues in contact with ILE 172 (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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141A ILE* 3.7 11.5 - - + +
155A ALA* 3.1 12.1 - - - +
156A GLY* 2.7 47.6 + - - +
158A HIS* 4.8 0.9 - - + -
170A GLU* 3.9 20.6 - - + +
171A VAL* 1.3 78.4 - - - +
173A LYS* 1.3 62.5 + - - +
182A PHE* 5.8 0.2 - - - -
199A CYS* 3.6 24.2 - - + +
200A LYS 3.8 0.2 - - - +
201A ASP* 3.6 30.7 - - + -
205A PHE* 3.6 49.4 - - + -
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Residues in contact with LYS 173 (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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171A VAL 3.8 1.0 + - - +
172A ILE* 1.3 76.7 - - - +
174A THR* 1.3 67.2 + - - +
175A PRO* 4.9 0.2 - - - +
177A THR* 3.5 40.2 - - + -
178A SER 4.3 1.6 - - - -
179A GLN* 2.9 36.6 + - - +
182A PHE* 4.1 36.4 - - + +
198A SER* 5.5 3.8 - - - +
199A CYS 3.4 8.5 + - - +
200A LYS* 4.0 5.3 - - - +
201A ASP 3.5 19.1 + - - -
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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