Contacts of the strand formed by residues 114 - 118 (chain A) in PDB entry 5UPE
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 ILE 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A LEU* 2.8 13.1 + - + +
113A PRO* 1.3 70.8 - - - +
115A GLU* 1.3 61.8 + - - +
116A ILE* 3.7 27.8 - - + -
134A VAL* 3.8 12.6 - - + -
135A GLU 3.4 12.3 - - - +
136A ASN* 4.0 8.1 - - - -
137A THR* 3.9 3.5 + - - +
144A LEU* 3.6 31.6 - - + +
145A THR* 3.8 34.1 - - - +
148A ILE* 4.0 14.8 - - + -
462A PHE* 3.7 14.5 - - + -
463A LYS* 3.3 3.3 - - - -
464A ASN* 3.0 24.0 + - - -
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Residues in contact with GLU 115 (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 ILE* 1.3 73.0 - - - +
116A ILE* 1.4 64.7 + - - +
117A LYS* 3.5 19.9 + - + +
133A THR* 3.8 1.6 + - - +
134A VAL* 3.6 3.6 - - - -
135A GLU* 2.8 57.6 + - + +
137A THR* 3.8 17.0 - - + +
460A THR* 2.8 33.1 + - + +
462A PHE 3.3 10.3 - - - +
463A LYS* 3.8 25.2 + - + +
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Residues in contact with ILE 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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62A LEU* 4.2 15.3 - - + -
66A LEU* 3.6 24.7 - - + -
70A LEU* 4.0 17.0 - - + -
114A ILE* 3.7 19.7 - - + -
115A GLU* 1.4 75.3 - - - +
117A LYS* 1.3 63.5 + - - +
132A PHE* 4.3 11.2 - - + -
133A THR 3.2 10.8 - - - +
134A VAL* 4.1 9.6 - - + -
148A ILE* 4.6 0.2 - - + -
152A LEU* 4.2 14.6 - - + -
460A THR* 3.5 2.8 - - - -
461A VAL* 2.8 44.2 + - + +
462A PHE* 2.8 27.1 + - + +
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Residues in contact with LYS 117 (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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34A TYR* 6.5 0.2 - - + -
115A GLU* 3.5 24.8 + - + +
116A ILE* 1.3 72.1 - - - +
118A ALA* 1.3 60.9 + - - +
132A PHE* 3.1 5.4 - - - +
133A THR* 2.8 47.1 + - - +
135A GLU* 4.9 9.4 + - - +
456A ASP* 5.1 7.5 + - - +
458A LEU* 4.1 23.4 - - + +
459A HIS 3.1 6.7 - - - +
460A THR* 3.5 33.2 - - - +
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Residues in contact with ALA 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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59A PHE* 4.1 4.3 - - + -
62A LEU* 3.7 21.3 - - + -
116A ILE 4.2 0.4 - - - -
117A LYS* 1.3 75.4 - - - +
119A VAL* 1.3 71.4 + - - +
120A PRO* 3.8 1.4 - - - +
131A LEU 3.4 6.1 - - - +
132A PHE* 3.7 15.0 - - + -
457A LEU 4.0 0.3 - - - +
458A LEU* 3.9 4.7 - - - -
459A HIS* 2.8 35.5 + - - +
461A VAL* 3.9 16.4 - - + +
471A TYR* 5.2 0.7 + - - -
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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