Contacts of the strand formed by residues 174 - 178 (chain A) in PDB entry 3U3D
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 PHE 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A PHE* 4.1 2.3 - - - -
78A TRP* 3.0 33.9 + - + -
138A ALA* 4.0 15.7 - - + -
139A VAL 3.4 16.6 - - - -
140A CYS* 3.5 16.8 - - + -
145A LYS* 3.9 20.0 - - + -
147A VAL* 3.5 32.8 - - + -
160A PHE* 4.3 10.1 - + + -
165A PRO* 4.2 1.9 - - - +
166A PRO* 2.8 26.3 + - + +
167A GLU 3.4 30.7 - - - -
168A CYS* 3.6 16.4 - - + -
169A PRO* 4.7 3.6 - - + -
173A ILE* 1.3 84.2 - - - +
175A LYS* 1.4 59.2 + - - +
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Residues in contact with LYS 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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67A ILE* 3.9 16.2 - - + -
70A PHE* 3.6 32.1 - - + -
71A TRP* 5.5 2.9 - - + -
78A TRP* 3.9 2.9 - - - -
138A ALA* 3.5 0.5 - - - -
139A VAL* 2.7 38.9 + - + +
141A CYS* 4.3 17.3 - - + -
173A ILE 3.7 0.2 + - - -
174A PHE* 1.4 73.9 - - - +
176A PRO* 1.3 83.0 + - + +
178A ILE* 3.6 23.0 + - - +
180A LEU* 4.1 11.4 - - + +
183A GLU* 3.4 28.2 + - - -
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Residues in contact with PRO 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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70A PHE* 4.4 1.6 - - + -
77A ILE* 3.7 40.8 - - + -
78A TRP* 3.6 27.8 - - + +
81A ILE* 4.1 15.3 - - + -
135A VAL* 5.3 3.8 - - + +
137A GLU 3.8 6.7 - - - +
175A LYS* 1.3 108.8 + - + +
177A ASN* 1.3 60.3 + - - +
178A ILE* 2.9 26.6 + - + +
180A LEU* 6.3 0.4 - - + -
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Residues in contact with ASN 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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133A GLY* 3.4 7.9 - - - -
134A ASN* 2.8 27.4 + - - +
137A GLU* 2.7 54.0 + - + +
139A VAL* 4.1 22.4 - - + +
175A LYS 3.5 0.6 + - - -
176A PRO* 1.3 73.7 - - - +
178A ILE* 1.3 59.0 + - - +
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Residues in contact with ILE 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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77A ILE* 3.3 29.6 - - + -
81A ILE* 4.4 7.0 - - + -
116A VAL* 3.9 17.7 - - + -
132A HIS 3.1 11.2 - - - +
134A ASN 3.7 24.0 - - - +
135A VAL* 3.9 8.1 - - + +
175A LYS* 3.6 12.0 + - - +
176A PRO* 2.9 17.9 + - + +
177A ASN* 1.3 82.6 - - - +
179A ILE* 1.3 68.2 + - - +
180A LEU* 3.7 15.3 + - + -
183A GLU* 3.5 9.2 - - - +
9B MYK 4.0 21.8 - - + -
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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