Contacts of the strand formed by residues 48 - 53 (chain A) in PDB entry 4UTX
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 HIS 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LYS* 1.3 96.0 + - + +
49A ILE* 1.3 59.7 + - - +
129A ARG* 6.2 0.2 - - - -
130A SER* 3.6 26.6 + - - +
132A VAL* 6.0 0.2 - - - -
234A GLU 5.8 0.2 - - - +
237A LYS* 3.4 38.0 - - + +
238A CYS* 3.2 10.2 - - + +
239A ASP* 2.8 38.5 + - - +
240A LEU 3.5 1.2 + - - -
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Residues in contact with ILE 49 (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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43A PHE* 4.0 24.2 - - + -
46A ALA* 3.6 33.0 - - + -
47A LYS 5.1 0.4 - - - -
48A HIS* 1.3 73.7 - - - +
50A ALA* 1.3 64.8 + - - +
51A ILE* 4.0 23.8 - - + -
120A CYS* 5.4 1.6 - - - -
124A LEU* 4.2 15.5 - - + -
130A SER* 2.9 15.9 + - - +
131A VAL* 3.3 8.9 - - + +
132A VAL* 3.0 29.6 + - - +
238A CYS* 4.7 0.7 - - - -
240A LEU* 3.5 27.4 - - + +
242A LEU* 4.8 7.9 - - + -
297A LEU* 6.1 0.4 - - + -
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Residues in contact with ALA 50 (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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48A HIS 4.2 0.4 + - - -
49A ILE* 1.3 74.4 - - - +
51A ILE* 1.3 64.7 + - - +
52A ILE* 4.1 0.4 - - - -
132A VAL* 3.4 13.9 - - + +
134A ILE* 4.3 8.7 - - + -
234A GLU 5.2 2.5 - - - +
235A LEU* 3.9 27.8 - - + -
238A CYS* 4.2 14.8 - - + -
240A LEU 3.1 6.7 + - - -
241A CYS* 3.2 7.3 - - - +
242A LEU 2.8 26.0 + - - +
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Residues in contact with ILE 51 (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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49A ILE* 4.0 13.0 - - + -
50A ALA* 1.3 80.0 - - - +
52A ILE* 1.3 63.7 + - - +
53A THR* 3.9 18.4 - - + -
117A ILE* 4.1 31.6 - - + -
120A CYS* 5.8 2.9 - - - -
131A VAL* 3.9 23.1 - - + -
132A VAL 2.9 12.5 + - - +
133A ILE* 3.3 9.7 - - + +
134A ILE* 2.8 25.7 + - - +
242A LEU* 3.5 23.1 - - + -
244A VAL* 4.1 19.7 - - + -
297A LEU* 5.2 4.9 - - + -
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Residues in contact with ILE 52 (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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50A ALA 5.4 0.2 - - - -
51A ILE* 1.3 74.3 - - - +
53A THR* 1.3 71.6 + - - +
134A ILE* 3.1 33.7 - - + +
136A GLN 6.2 0.2 - - - +
235A LEU* 4.9 7.6 - - + -
241A CYS* 3.7 28.7 - - - -
242A LEU 2.8 10.1 + - - +
243A VAL* 3.4 12.1 - - + +
244A VAL* 2.8 27.4 + - - +
246A THR* 4.9 7.0 - - + -
252A PRO* 5.0 8.3 - - + -
253A ALA* 4.6 27.6 - - + +
256A PHE* 4.8 21.5 - - + -
257A ALA* 5.3 2.9 - - + +
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Residues in contact with THR 53 (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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51A ILE* 3.9 19.5 - - + -
52A ILE* 1.3 84.2 - - - +
54A GLY* 1.3 59.8 - - - +
57A VAL* 4.3 7.0 - - + -
117A ILE* 4.7 2.9 - - + -
133A ILE* 4.2 8.3 - - + -
134A ILE 3.0 6.5 + - - -
135A THR* 2.7 35.2 + - - -
136A GLN* 3.1 23.9 + - - +
137A ASN* 3.5 5.0 + - - -
142A HIS* 3.1 28.4 + - + +
244A VAL* 3.3 14.1 - - + -
246A THR* 4.2 2.5 - - - -
252A PRO* 6.3 0.4 - - - -
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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