Contacts of the strand formed by residues 103 - 108 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C HIS* 4.4 1.1 - - - -
98C VAL 4.1 0.2 - - - +
99C SER* 3.3 7.8 + - - -
100C TRP* 2.8 69.4 + - + +
102C ASP* 1.3 80.4 - - + +
104C ILE* 1.3 64.7 + - - +
105C VAL* 4.2 7.6 - - + +
132C LEU* 5.7 0.7 - - + -
133C ALA 3.3 16.4 - - - +
134C GLN* 4.1 13.7 - - + +
200C VAL* 3.8 17.5 - - + -
204C PHE* 3.5 31.4 - - + -
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Residues in contact with ILE 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C HIS* 3.7 30.3 - - + +
36C VAL* 3.8 28.9 - - + -
53C VAL* 4.9 2.9 - - + -
55C LEU* 3.9 15.3 - - + -
68C LEU* 3.9 27.4 - - + -
70C PHE* 4.9 1.5 - - + -
97C VAL* 5.4 0.2 - - + -
98C VAL 3.5 6.3 - - - +
99C SER* 4.5 0.9 - - - +
103C VAL* 1.3 78.0 - - - +
105C VAL* 1.3 68.1 + - - +
106C ALA* 3.9 3.8 + - + +
131C PHE 3.7 1.2 - - - +
132C LEU* 3.6 2.6 - - - -
133C ALA* 2.9 36.4 + - + +
135C PRO* 3.6 24.7 - - + -
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C SER 4.0 0.2 - - - +
97C VAL* 3.2 4.9 - - - +
98C VAL* 2.7 53.1 + - + +
100C TRP* 5.8 1.8 - - + +
103C VAL* 5.2 7.0 - - + +
104C ILE* 1.3 76.6 - - - +
106C ALA* 1.3 60.6 + - - +
107C CYS* 4.1 8.3 - - - -
130C CYS* 4.0 14.8 - - + -
131C PHE 3.5 5.6 - - - +
132C LEU* 3.4 31.9 - - + -
173C SER* 5.6 0.2 - - - +
175C VAL* 4.7 7.2 - - + -
181C LEU* 4.0 28.5 - - + -
200C VAL* 5.3 5.4 - - + -
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Residues in contact with ALA 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C VAL* 3.4 34.3 - - + -
70C PHE* 4.3 11.2 - - + -
93C LEU* 4.1 7.2 - - + -
94C GLY 4.8 0.7 - - - +
96C SER 3.4 4.5 - - - +
97C VAL* 4.1 8.3 - - + -
104C ILE* 3.9 3.1 + - + -
105C VAL* 1.3 74.6 - - - +
107C CYS* 1.3 59.7 + - - +
131C PHE* 2.7 47.4 + - - +
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Residues in contact with CYS 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C GLY 3.1 4.0 - - - +
93C LEU* 4.2 1.3 - - - -
94C GLY 2.8 26.0 + - - -
95C ALA 3.4 5.4 + - - -
96C SER* 3.0 19.2 + - - -
105C VAL* 4.1 11.2 - - - -
106C ALA* 1.3 76.6 - - - +
108C ALA* 1.3 61.7 + - - +
109C PRO* 3.7 2.7 - - - +
129C SER 3.4 4.5 - - - +
130C CYS* 2.0 47.1 - - - -
170C GLY* 3.6 28.9 - - - +
173C SER* 4.7 3.8 - - - -
183C LEU* 4.5 3.4 - - - -
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Residues in contact with ALA 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C GLN* 3.4 44.2 - - + +
92C GLY 3.5 1.3 - - - -
93C LEU* 3.7 10.5 - - + +
107C CYS* 1.3 74.9 - - - +
109C PRO* 1.3 60.2 - - - +
110C TRP 3.1 9.6 + - - -
111C GLN* 3.3 5.7 + - + +
128C GLY* 3.3 3.1 - - - -
129C SER 2.8 31.0 + - - +
131C PHE* 4.3 7.9 - - + -
169C ALA 4.5 0.4 - - - -
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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