Contacts of the strand formed by residues 174 - 179 (chain A) in PDB entry 3FHC
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 ILE 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ALA* 4.6 4.3 - - + -
167A VAL 3.1 16.6 - - - +
168A CYS* 4.8 0.4 - - - -
169A LEU* 5.8 1.3 - - - -
173A SER* 1.3 76.0 - - - +
175A ALA* 1.3 80.1 + - - +
176A VAL* 4.9 3.6 - - + -
188A THR* 3.2 5.1 - - - -
189A LEU* 2.9 65.0 + - + +
195A VAL* 4.1 17.5 - - + -
198A VAL* 3.8 13.7 - - + -
207A LEU* 3.7 19.3 - - + -
209A VAL* 3.6 28.0 - - + -
223A LEU* 4.9 4.7 - - + -
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Residues in contact with ALA 175 (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 HIS* 5.9 0.9 - - - +
144A LEU* 5.8 4.7 - - + -
165A VAL 3.9 0.5 - - - +
166A ALA* 3.5 1.7 - - - -
167A VAL* 2.9 39.7 + - + +
174A ILE* 1.3 79.2 - - - +
176A VAL* 1.3 65.3 + - - +
177A LEU* 4.1 19.6 + - + +
185A VAL* 4.6 1.1 - - + -
187A ALA 3.2 5.8 - - - +
188A THR* 3.6 20.4 - - + -
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A MET* 4.1 17.7 - - + -
165A VAL 3.5 9.4 - - - +
166A ALA* 4.4 1.1 - - + +
174A ILE* 4.9 2.5 - - + -
175A ALA* 1.3 76.3 - - - +
177A LEU* 1.3 66.9 + - - +
185A VAL* 3.9 0.7 - - - +
186A CYS* 3.0 29.9 + - + +
187A ALA* 2.6 23.5 + - + +
200A TRP* 4.0 24.5 - - + -
207A LEU* 4.4 13.0 - - + -
221A PRO 3.9 23.3 - - - +
223A LEU* 4.0 23.1 - - + -
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Residues in contact with LEU 177 (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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120A ILE* 4.6 1.1 - - + -
122A PHE* 4.3 16.2 - - + -
142A HIS* 4.1 24.7 - - + +
144A LEU* 4.9 0.7 - - + -
163A SER 3.5 0.6 - - - +
164A MET* 3.3 8.5 - - - +
165A VAL* 2.8 44.3 + - + +
167A VAL* 4.1 22.4 - - + -
175A ALA* 4.1 19.1 - - + +
176A VAL* 1.3 79.6 - - - +
178A GLN* 1.3 62.0 + - - +
179A VAL* 4.2 1.3 - - + -
183A VAL* 4.2 13.5 - - + -
184A LYS 3.3 5.2 - - - +
185A VAL* 3.4 33.0 - - + -
186A CYS* 4.1 4.2 - - - -
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Residues in contact with GLN 178 (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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163A SER* 3.1 23.8 + - - +
164A MET* 5.1 9.1 - - + +
177A LEU* 1.3 75.4 - - - +
179A VAL* 1.3 63.0 + - - +
180A THR* 3.7 21.7 + - + +
182A THR 3.3 2.4 - - - +
183A VAL* 3.6 0.5 - - - -
184A LYS* 2.7 62.1 + - + +
186A CYS* 3.7 17.9 - - - -
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Residues in contact with VAL 179 (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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106A THR* 4.9 3.4 - - + +
122A PHE* 3.9 26.9 - - + -
139A PHE* 3.4 37.0 - - + -
157A TRP* 4.4 11.4 - - + -
163A SER* 2.6 34.5 + - - +
165A VAL* 4.9 4.9 - - + -
177A LEU* 5.0 0.9 - - + -
178A GLN* 1.3 77.7 - - - +
180A THR* 1.3 64.8 + - - +
182A THR 3.3 6.7 - - - +
183A VAL* 3.6 30.1 - - + -
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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
------------------------------------------------------------
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