Contacts of the strand formed by residues 123 - 127 (chain A) in PDB entry 1UFK
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 LYS 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A GLY 4.5 5.4 - - - +
122A ASP* 1.3 73.9 - - - +
124A VAL* 1.3 60.4 + - - +
144A LYS* 3.2 20.2 + - + +
182A PHE* 3.4 25.1 + - - +
184A PRO 4.5 9.2 + - - +
185A PHE* 3.5 19.5 - - + +
186A ASP* 2.8 46.3 + - - +
187A LEU 3.2 6.9 + - - -
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Residues in contact with VAL 124 (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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114A LEU* 5.1 1.1 - - + -
118A LEU* 3.4 39.9 - - + -
122A ASP 4.1 5.2 - - - +
123A LYS* 1.3 79.2 - - - +
125A LEU* 1.3 74.0 + - - +
126A ASP* 4.3 3.1 - - + +
138A ALA* 4.3 15.5 - - + -
144A LYS 2.8 10.9 + - - +
145A ALA* 3.4 12.5 - - + -
146A LEU* 2.8 28.6 + - - +
185A PHE* 3.8 8.5 - - - -
187A LEU* 3.2 24.0 - - + +
189A VAL* 4.3 9.2 - - + -
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Residues in contact with LEU 125 (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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124A VAL* 1.3 76.5 - - - +
126A ASP* 1.3 55.0 + - - +
127A LEU* 4.2 11.0 - - + +
146A LEU* 3.4 22.4 - - + +
148A VAL* 4.1 18.2 - - + -
176A LEU* 3.5 32.3 - - + -
179A ALA* 3.7 27.4 - - + -
185A PHE* 3.9 25.3 - - + -
187A LEU 2.9 9.6 + - - +
188A LEU* 3.3 17.7 - - + -
189A VAL* 2.8 33.6 + - - +
207A ALA* 5.0 0.9 - - + -
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Residues in contact with ASP 126 (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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124A VAL* 4.0 3.3 + - + -
125A LEU* 1.3 72.5 - - - +
127A LEU* 1.3 64.1 + - - +
128A GLY 3.5 2.8 + - - +
129A THR* 2.6 35.3 + - - +
134A LEU* 3.5 28.4 + - - +
135A ALA* 3.2 31.2 + - + +
145A ALA* 5.8 0.2 - - + -
146A LEU 2.9 13.3 + - - +
147A GLY* 4.1 0.9 - - - -
148A VAL 3.1 24.6 + - - +
189A VAL* 3.4 16.9 - - + +
190A ALA* 5.3 0.3 - - - -
191A ASN 5.5 0.5 + - - -
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Residues in contact with LEU 127 (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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125A LEU* 3.7 11.5 - - + -
126A ASP* 1.3 69.5 - - - +
128A GLY* 1.3 66.4 + - - +
148A VAL* 3.5 24.5 - - + -
174A GLY 5.3 0.4 - - - +
175A SER* 4.0 7.9 - - - +
176A LEU* 3.8 35.0 - - + +
188A LEU* 5.1 2.7 - - + -
189A VAL 2.8 14.2 + - - +
190A ALA* 3.7 20.2 - - + -
191A ASN 3.9 3.1 + - - -
192A LEU* 3.9 28.6 - - + +
200A LEU* 4.1 10.1 - - + -
204A TYR* 3.9 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