Contacts of the strand formed by residues 113 - 118 (chain A) in PDB entry 3UJK
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 TYR 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A PRO* 4.2 25.1 - - + -
112A LEU* 1.3 77.5 - - - +
114A GLY* 1.3 65.3 + - - +
115A VAL* 4.6 3.4 - - + -
131A THR* 3.4 49.8 + - + -
133A PRO* 4.1 19.0 - - + +
161A PHE* 3.7 27.1 - + + -
379A GLY 4.7 12.9 - - - -
380A LYS* 3.6 33.7 + - + +
381A ASP* 2.8 28.4 + - - +
384A ALA* 3.4 7.4 - - - -
407A VAL* 5.1 0.2 - - + -
408A VAL 3.2 11.9 - - - +
409A VAL* 4.2 3.6 - - + -
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Residues in contact with GLY 114 (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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113A TYR* 1.3 78.2 - - - +
115A VAL* 1.3 65.3 + - - +
384A ALA* 3.4 3.6 - - - +
385A MET* 3.5 30.1 - - - -
388A ALA* 4.1 6.3 - - - -
407A VAL* 3.4 6.4 - - - +
408A VAL 2.9 29.5 + - - +
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TYR* 4.6 2.7 - - + -
114A GLY* 1.3 77.4 - - - +
116A THR* 1.3 69.7 + - - +
117A SER* 4.9 0.4 - - - +
129A VAL* 3.9 26.7 - - + -
131A THR* 3.9 22.7 - - + +
380A LYS* 4.2 28.3 - - + +
385A MET* 3.4 20.6 - - - +
388A ALA* 4.0 4.9 - - - +
389A GLU* 5.1 2.1 - - - +
406A VAL 3.3 12.1 - - - +
407A VAL* 3.8 15.9 - - + -
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Residues in contact with THR 116 (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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115A VAL* 1.3 78.2 - - - +
117A SER* 1.3 62.7 + - - +
118A ILE* 3.8 15.9 - - - +
388A ALA 3.2 34.1 - - - +
389A GLU* 4.3 13.2 - - - +
392A SER* 3.7 19.6 - - - -
404A ILE 4.3 1.8 - - - +
405A SER* 3.3 1.6 - - - -
406A VAL* 2.8 47.9 + - + +
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 5.2 0.4 - - - -
116A THR* 1.3 76.5 + - - +
118A ILE* 1.3 64.0 + - - +
125A MET* 3.2 18.2 - - - +
127A ASP* 4.2 5.0 + - - +
128A SER* 4.8 0.9 - - - -
129A VAL* 3.8 28.0 - - - +
404A ILE 3.4 5.2 - - - -
405A SER* 2.8 19.7 + - - -
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Residues in contact with ILE 118 (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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116A THR* 3.8 15.7 - - - +
117A SER* 1.3 78.8 - - - +
119A CYS* 1.3 58.6 + - - +
120A GLY* 3.9 15.3 - - - +
125A MET* 3.4 12.4 - - - +
392A SER* 3.2 22.7 - - - +
396A LEU* 3.9 24.7 - - + -
403A ASN* 3.5 1.6 - - - -
404A ILE* 2.9 50.4 + - + +
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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