Contacts of the strand formed by residues 48 - 53 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LYS* 1.3 93.5 + - + +
49B ILE* 1.3 60.8 + - - +
130B SER* 3.6 25.1 + - - +
132B VAL* 5.9 0.9 - - + -
234B GLU* 5.7 1.0 + - - +
237B LYS* 3.4 44.4 - - + +
238B CYS* 3.1 10.0 - - + +
239B ASP* 2.8 38.0 + - - +
240B LEU 3.6 1.0 + - - -
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Residues in contact with ILE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B PHE* 4.0 24.0 - - + +
46B ALA* 3.5 33.7 - - + -
47B LYS 5.1 0.2 - - - -
48B HIS* 1.3 74.8 - - - +
50B ALA* 1.3 65.5 + - - +
51B ILE* 4.0 24.0 - - + -
120B CYS* 5.5 1.6 - - - -
124B LEU* 4.1 15.9 - - + -
130B SER* 2.9 15.0 + - - +
131B VAL* 3.3 8.6 - - + +
132B VAL* 3.0 29.2 + - - +
238B CYS* 4.7 0.4 - - - -
240B LEU* 3.5 26.9 - - + +
242B LEU* 4.8 9.0 - - + -
297B LEU* 6.2 0.2 - - + -
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B HIS 4.1 0.4 + - - -
49B ILE* 1.3 74.1 - - - +
51B ILE* 1.3 63.2 + - - +
52B ILE* 4.1 0.9 - - + -
132B VAL* 3.4 13.9 - - + +
134B ILE* 4.3 9.2 - - + -
234B GLU* 5.3 2.5 - - + +
235B LEU* 3.9 28.0 - - + -
238B CYS* 4.2 15.7 - - + -
240B LEU 3.1 7.3 + - - -
241B CYS* 3.2 7.4 - - + +
242B LEU 2.8 25.6 + - - +
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 4.0 13.2 - - + -
50B ALA* 1.3 80.0 - - - +
52B ILE* 1.3 63.0 + - - +
53B THR* 3.9 17.7 - - + -
117B ILE* 4.1 31.4 - - + -
120B CYS* 5.9 2.5 - - - -
131B VAL* 3.9 22.0 - - + -
132B VAL 2.9 12.3 + - - +
133B ILE* 3.3 9.4 - - + +
134B ILE* 2.9 25.7 + - - +
242B LEU* 3.5 24.0 - - + -
244B VAL* 4.1 20.2 - - + -
297B LEU* 5.2 6.7 - - + -
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Residues in contact with ILE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ALA 5.3 0.4 - - - -
51B ILE* 1.3 76.5 - - - +
53B THR* 1.3 67.9 + - - +
134B ILE* 3.1 32.1 - - + +
136B GLN* 5.3 5.4 - - + +
235B LEU* 5.1 2.5 - - + -
241B CYS* 3.7 28.5 - - - -
242B LEU 2.8 8.8 + - - +
243B VAL* 3.4 12.3 - - + -
244B VAL* 2.8 27.9 + - - +
246B THR* 4.9 4.5 - - + -
253B ALA* 4.4 25.6 - - + +
256B PHE* 3.7 33.9 - - + -
257B ALA* 4.2 5.6 - - + +
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Residues in contact with THR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ILE* 3.9 19.3 - - + -
52B ILE* 1.3 82.2 - - - +
54B GLY* 1.3 59.5 + - - +
57B VAL* 4.1 10.1 - - + -
117B ILE* 4.6 3.1 - - + -
133B ILE* 4.2 8.1 - - + -
134B ILE 3.0 6.9 + - - -
135B THR* 2.7 27.2 + - - -
136B GLN* 3.2 26.9 + - - +
137B ASN* 3.6 3.0 + - - -
142B HIS* 3.1 29.0 + - + +
244B VAL* 3.3 13.7 - - + -
246B THR* 4.3 1.6 - - - -
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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