Contacts of the strand formed by residues 173 - 177 (chain A) in PDB entry 3F9C
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 3.6 29.8 - - + -
84A TYR 3.4 6.7 - - - +
85A TYR* 4.0 15.5 - - + -
86A PRO* 4.2 0.7 - - + -
138A LEU* 4.2 11.4 - - + -
144A TYR* 3.6 33.4 - - + +
145A PRO 3.2 8.6 + - - +
146A LEU* 3.4 19.8 - - + +
147A VAL 2.9 25.1 + - - -
172A PHE* 1.3 74.9 - - - +
174A VAL* 1.3 64.6 + - - +
236A ILE* 5.8 1.3 - - + -
258A LEU* 4.3 8.3 - - + -
261A SER* 4.0 10.8 - - - +
262A ILE* 3.9 24.0 - - + -
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Residues in contact with VAL 174 (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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82A ARG 3.5 1.4 - - - +
83A LEU* 3.1 11.6 - - - +
84A TYR* 2.8 59.4 + - + +
147A VAL* 3.5 16.4 - - + +
149A PHE* 4.2 24.2 - - + -
164A GLY* 3.8 17.5 - - - +
167A LEU* 3.7 36.8 - - + -
168A ALA 4.4 1.8 - - - +
172A PHE* 4.3 6.3 - - + -
173A ILE* 1.3 77.9 - - - +
175A ALA* 1.3 63.1 + - - +
176A ALA* 4.4 0.9 - - + +
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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
----------------------------------------------------------
81A LEU* 3.9 15.0 - - + -
82A ARG 3.7 4.0 - - - -
83A LEU* 4.1 8.5 - - + -
146A LEU* 4.5 4.0 - - + +
147A VAL 2.9 12.1 + - - +
148A VAL* 3.5 14.2 - - + +
149A PHE 2.8 24.0 + - - -
173A ILE 4.2 0.4 - - - -
174A VAL* 1.3 72.4 - - - +
176A ALA* 1.3 62.8 + - - +
177A VAL* 3.5 3.6 + - + +
232A ALA* 5.4 0.2 - - + -
236A ILE* 3.8 29.2 - - + -
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Residues in contact with ALA 176 (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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81A LEU* 3.1 2.3 - - - -
82A ARG* 2.8 42.8 + - + +
84A TYR* 4.1 15.5 - - + -
149A PHE* 3.6 25.4 - - + +
157A ARG* 3.4 27.7 - - + +
160A TYR* 6.1 2.5 - - + -
174A VAL* 3.8 2.3 - - + -
175A ALA* 1.3 69.4 - - - +
177A VAL* 1.3 64.0 + - - +
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Residues in contact with VAL 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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79A THR* 5.6 1.3 - - + -
80A PHE 3.5 10.5 - - - +
81A LEU* 4.2 4.9 - - + -
148A VAL* 4.0 21.8 - - + -
149A PHE 3.0 15.5 + - - +
151A HIS* 3.1 20.6 + - - +
157A ARG* 3.7 6.4 - - - +
175A ALA* 4.1 3.4 - - + +
176A ALA* 1.3 74.7 - - - +
178A GLU* 1.3 73.6 + - - +
179A HIS* 3.9 24.2 - - + +
228A GLU* 4.3 16.4 - - + +
229A CYS* 4.7 2.2 - - - -
232A ALA* 3.6 29.2 - - + -
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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