Contacts of the strand formed by residues 146 - 150 (chain C) in PDB entry 3HYW
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 146 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139C LEU* 3.7 28.5 - - + -
145C PRO* 1.3 77.4 - - - +
147C VAL* 1.3 66.7 + - - +
148C ILE* 3.7 32.5 - - + -
167C LEU* 3.8 12.3 - - + -
180C VAL* 3.5 24.0 - - + -
181C PRO 2.8 12.5 + - - +
182C MET* 3.4 11.4 - - + -
183C THR* 3.0 25.1 + - - +
247C PHE* 3.3 16.2 - - + -
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Residues in contact with VAL 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C PRO* 5.5 0.2 - - + -
146C VAL* 1.3 78.1 - - - +
148C ILE* 1.3 65.1 + - - +
183C THR* 3.4 11.0 - - - +
185C ILE* 3.7 30.5 - - + -
231C VAL* 3.8 15.3 - - + -
243C VAL* 3.4 27.6 - - + -
244C PRO 3.6 4.0 - - - +
245C ALA* 3.5 21.1 - - + -
247C PHE 3.0 6.3 + - - -
248C THR* 3.1 28.3 - - + -
249C MET 3.1 2.8 + - - -
250C PHE* 3.7 18.4 - - + -
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Residues in contact with ILE 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C VAL* 3.7 23.1 - - + -
147C VAL* 1.3 79.3 - - - +
149C GLY* 1.3 65.7 + - - +
160C ALA* 3.6 23.1 - - + +
163C PHE* 3.7 17.0 - - + -
164C ALA* 3.6 26.7 - - + -
167C LEU* 4.0 6.5 - - + -
182C MET* 4.1 4.9 - - + -
183C THR 2.9 8.4 + - - +
184C PHE* 3.1 16.8 - - + -
185C ILE 2.8 23.4 + - - -
247C PHE* 5.0 0.4 - - + -
249C MET* 3.2 35.2 - - + +
250C PHE* 4.0 6.1 - - - -
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Residues in contact with GLY 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ILE* 1.3 85.5 - - - +
150C ALA* 1.3 61.0 + - - -
160C ALA* 4.1 5.1 - - - +
184C PHE* 4.2 12.8 - - - -
185C ILE 3.1 10.5 - - - -
249C MET 3.1 5.5 + - - +
250C PHE* 3.3 11.6 - - - -
251C MET* 2.9 30.1 + - - +
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Residues in contact with ALA 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C GLY* 1.3 75.3 - - - +
151C ILE* 1.3 64.5 + - - +
154C VAL* 3.9 14.4 - - + -
157C PHE* 3.5 39.5 - - + -
160C ALA* 5.4 1.6 - - + -
184C PHE* 5.9 0.9 - - + -
185C ILE 2.9 11.4 + - - +
186C THR* 3.7 7.7 - - - +
187C SER* 3.4 16.0 + - - +
223C VAL* 4.0 8.1 + - - +
250C PHE* 3.4 3.9 - - - -
251C MET* 4.3 6.1 - - + -
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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