Contacts of the strand formed by residues 103 - 108 (chain E) in PDB entry 1TYE
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 VAL 103 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26E HIS* 4.5 0.2 - - - -
98E VAL 4.1 0.2 - - - +
99E SER* 3.4 5.2 + - - -
100E TRP* 2.9 51.5 + - + +
102E ASP* 1.3 84.7 - - + +
104E ILE* 1.3 77.7 + - - +
105E VAL* 3.8 15.4 - - + +
132E LEU* 4.2 6.3 - - + -
133E ALA 3.4 11.4 - - - +
134E GLN* 4.8 7.4 - - + +
200E VAL* 3.8 31.4 - - + -
204E PHE* 4.3 13.5 - - + -
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Residues in contact with ILE 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E HIS* 3.7 26.7 - - + +
36E VAL* 3.9 26.7 - - + -
53E VAL* 4.8 3.6 - - + -
55E LEU* 3.7 40.2 - - + -
68E LEU* 3.7 28.9 - - + -
70E PHE* 5.3 1.6 - - + -
98E VAL 3.7 5.4 - - - +
99E SER* 4.6 1.1 - - - -
103E VAL* 1.3 77.3 - - - +
105E VAL* 1.3 69.6 + - - +
106E ALA* 4.1 4.0 - - + +
131E PHE 3.9 0.5 - - - +
132E LEU* 3.6 2.3 - - - -
133E ALA* 2.9 35.4 + - + +
135E PRO* 3.9 10.1 - - + -
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Residues in contact with VAL 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E SER 3.8 0.5 - - - +
97E VAL* 3.1 4.7 - - - +
98E VAL* 2.8 56.7 + - + +
100E TRP* 6.1 0.9 - - + +
103E VAL* 3.8 9.6 - - + +
104E ILE* 1.3 79.3 - - - +
106E ALA* 1.3 61.0 + - - +
107E CYS* 4.1 20.4 - - - -
130E CYS* 4.2 8.5 - - + -
131E PHE 3.6 8.7 - - - +
132E LEU* 3.6 25.1 - - + -
175E VAL* 4.9 6.5 - - + -
181E LEU* 4.1 26.5 - - + -
200E VAL* 5.1 2.9 - - + -
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Residues in contact with ALA 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E VAL* 3.4 35.0 - - + -
70E PHE* 4.4 9.2 - - + -
93E LEU* 3.9 10.3 - - + -
94E GLY 4.7 0.7 - - - +
96E SER 3.4 4.9 - - - -
97E VAL* 4.2 9.4 - - + -
104E ILE* 4.1 3.7 - - + +
105E VAL* 1.3 75.0 - - - +
107E CYS* 1.3 58.3 + - - +
130E CYS* 3.5 0.5 - - - -
131E PHE* 2.7 39.8 + - - +
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Residues in contact with CYS 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E GLY 3.2 3.5 - - - +
93E LEU* 4.1 2.0 - - - -
94E GLY 2.8 24.8 + - - +
95E ALA 3.5 4.5 + - - -
96E SER* 2.9 20.4 + - - +
105E VAL* 4.1 11.0 - - - -
106E ALA* 1.3 76.4 - - - +
108E ALA* 1.3 62.6 + - - +
109E PRO* 3.9 2.2 - - - +
129E SER 3.4 4.3 - - - +
130E CYS* 2.0 46.2 - - - -
170E GLY* 3.6 27.6 - - - +
173E SER* 4.6 3.1 - - - -
183E LEU* 4.5 4.5 - - - -
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Residues in contact with ALA 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E GLN* 3.1 43.1 - - + +
92E GLY 3.7 1.1 - - - -
93E LEU* 3.6 11.2 - - + -
107E CYS* 1.3 74.8 - - - +
109E PRO* 1.3 69.2 - - - +
110E TRP 3.1 3.6 + - - -
111E GLN* 3.2 8.3 + - + +
129E SER 2.7 30.5 + - - +
131E PHE* 4.2 5.6 - - + -
169E ALA 4.5 0.2 - - - -
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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