Contacts of the strand formed by residues 111 - 115 (chain A) in PDB entry 5T0I
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ILE* 5.0 8.7 - - + -
104A ALA 3.9 8.1 - - - +
105A ASP* 3.4 25.5 + - + -
107A GLU 3.3 11.0 - - - -
108A ASP* 3.0 31.0 + - - +
109A PRO 4.8 2.7 - - - -
110A LYS* 1.3 82.4 - - - +
112A ILE* 1.3 64.1 + - - +
113A ILE* 3.9 11.3 + - + +
121A PHE 3.9 0.2 - - - +
122A VAL* 3.2 5.8 - - - -
123A VAL 2.9 33.5 + - - +
125A LEU* 3.9 15.0 - - + -
131A PRO* 3.5 21.8 + - - +
134A ILE* 3.6 40.0 + - + -
136A GLU* 5.5 0.7 - - - -
149A ILE* 4.4 11.9 - - + -
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Residues in contact with ILE 112 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ILE* 3.3 6.2 - - - +
103A ASN* 2.8 52.3 + - + +
104A ALA* 3.4 34.0 + - + +
111A TYR* 1.3 72.2 - - - +
113A ILE* 1.3 60.7 + - - +
120A LYS* 4.3 24.2 - - + -
121A PHE 4.6 0.7 - - - +
122A VAL* 3.6 25.5 - - + +
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Residues in contact with ILE 113 (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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100A LYS* 3.5 48.0 - - + -
101A ILE 3.2 25.1 - - - +
102A ILE* 3.6 17.7 - - + -
103A ASN* 4.0 3.4 - - - -
111A TYR* 4.0 8.3 - - + +
112A ILE* 1.3 80.9 - - - +
114A ASN* 1.3 57.6 + - - +
120A LYS* 3.2 2.9 - - - +
121A PHE* 2.3 54.1 + - + +
123A VAL* 3.7 15.3 - - + +
140A VAL* 4.7 0.9 - - + -
149A ILE* 3.7 29.4 - - + -
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Residues in contact with ASN 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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100A LYS* 3.1 3.4 - - - -
101A ILE* 2.4 74.9 + - + +
103A ASN* 4.0 14.6 + - - +
113A ILE* 1.3 70.0 - - - +
115A VAL* 1.3 85.2 + - - +
118A PHE* 4.0 6.7 + - - +
119A ALA 3.6 8.8 - - - +
120A LYS* 3.5 28.2 - - + +
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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
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98A CYS* 3.8 28.0 - - + +
99A THR 3.3 16.2 - - - +
100A LYS* 3.6 17.3 - - + +
114A ASN* 1.3 87.7 + - - +
116A LYS* 1.3 67.2 + - - +
117A GLN* 3.5 25.1 - - + +
118A PHE* 2.9 19.8 + - - -
119A ALA 3.2 18.2 + - - +
121A PHE* 3.5 21.1 - - + -
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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