Contacts of the strand formed by residues 173 - 177 (chain C) in PDB entry 3F98
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 173 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LEU* 3.5 31.4 - - + -
84C TYR 3.5 5.6 - - - +
85C TYR* 3.9 14.6 - - + -
86C PRO* 4.0 6.5 - - + -
138C LEU* 4.2 5.2 - - + -
144C TYR* 3.7 26.0 - - + -
145C PRO 3.0 10.6 + - - +
146C LEU* 3.3 18.8 - - + +
147C VAL 2.9 24.4 + - - -
171C GLY 4.3 0.4 + - - -
172C PHE* 1.3 75.6 - - - +
174C VAL* 1.3 64.2 + - - +
236C ILE* 5.5 0.7 - - + -
258C LEU* 4.0 13.0 - - + -
261C SER* 4.0 11.4 - - - +
262C ILE* 3.7 24.9 - - + -
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Residues in contact with VAL 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ARG 3.5 1.7 - - - +
83C LEU* 3.3 8.1 - - - +
84C TYR* 2.9 58.3 + - + +
147C VAL* 3.3 21.3 - - + +
149C PHE* 4.3 15.7 - - + -
164C GLY* 3.7 17.9 - - - +
167C LEU* 3.6 36.8 - - + -
168C ALA 4.3 2.2 - - - +
172C PHE* 4.1 6.5 - - + +
173C ILE* 1.3 78.5 - - - +
175C ALA* 1.3 62.5 + - - +
176C ALA* 4.6 1.1 - - + +
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Residues in contact with ALA 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 4.2 15.0 - - + -
82C ARG 3.6 4.5 - - - -
83C LEU* 4.1 8.3 - - + -
146C LEU* 4.5 1.9 - - + +
147C VAL 2.8 13.2 + - - +
148C VAL* 3.4 11.1 - - + +
149C PHE 2.8 24.3 + - - -
174C VAL* 1.3 71.9 - - - +
176C ALA* 1.3 61.5 + - - +
177C VAL* 3.5 3.8 + - + +
232C ALA* 5.3 0.2 - - + -
236C ILE* 3.4 33.2 - - + -
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Residues in contact with ALA 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 3.2 1.2 - - - -
82C ARG* 2.7 43.7 + - + +
84C TYR* 4.1 16.6 - - + -
149C PHE* 3.5 24.2 - - + +
157C ARG* 3.4 27.8 - - - +
160C TYR* 6.0 2.2 - - + +
174C VAL* 3.9 1.9 + - + -
175C ALA* 1.3 68.9 - - - +
177C VAL* 1.3 65.8 + - - +
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Residues in contact with VAL 177 (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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79C THR* 5.7 1.1 - - + -
80C PHE 3.5 11.4 - - - +
81C LEU* 4.1 4.7 - - + -
148C VAL* 3.7 22.7 - - + -
149C PHE 3.0 13.4 + - - +
151C HIS* 3.2 20.1 + - - +
157C ARG* 3.7 5.3 - - - +
175C ALA 4.0 3.6 - - - +
176C ALA* 1.3 75.9 - - - +
178C GLU* 1.3 74.9 + - - +
179C HIS* 4.0 24.0 - - + +
228C GLU* 4.3 17.7 - - + +
229C CYS* 4.6 2.9 - - - -
232C ALA* 3.6 28.5 - - + -
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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