Contacts of the strand formed by residues 53 - 57 (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 53 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C VAL* 3.6 26.9 - - + -
37C VAL 3.4 11.9 - - - +
52C GLY* 1.3 79.4 - - - +
54C PHE* 1.3 72.9 + - - +
67C SER* 3.9 5.0 + - - -
68C LEU* 3.1 39.6 + - + +
70C PHE* 3.8 22.9 - - + -
93C LEU* 4.3 4.4 - - + +
94C GLY* 4.2 10.8 - - - -
97C VAL* 4.1 6.5 - - + -
104C ILE* 4.9 0.2 - - + -
106C ALA* 3.4 29.8 - - + -
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Residues in contact with PHE 54 (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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13C GLY* 5.4 0.4 - - - -
14C PRO* 3.7 28.3 - - + -
19C PHE* 3.7 33.9 - + + -
35C ILE 3.6 1.1 - - - +
36C VAL* 3.5 4.3 - - - +
37C VAL* 2.9 36.9 + - + +
39C ALA* 3.9 25.1 - - + -
42C THR* 4.1 13.7 - - + -
52C GLY* 4.8 1.1 - - - -
53C VAL* 1.3 87.0 - - - +
55C LEU* 1.3 59.9 + - - +
56C CYS* 3.9 1.1 - - - -
65C CYS* 3.5 36.8 - - + -
66C PRO 3.5 8.5 - - - +
67C SER* 4.1 16.2 - - - -
68C LEU* 4.3 1.6 - - - +
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Residues in contact with LEU 55 (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* 4.0 20.6 - - + -
34C ALA* 4.3 11.4 - - + -
35C ILE 4.1 9.9 - - - +
36C VAL* 4.2 11.9 - - + -
54C PHE* 1.3 72.8 - - - +
56C CYS* 1.3 61.6 + - - +
57C PRO* 3.5 4.0 - - - +
66C PRO* 3.0 37.1 + - + +
68C LEU* 4.6 17.6 - - + +
104C ILE* 3.9 30.5 - - + -
135C PRO* 4.2 17.5 - - + -
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Residues in contact with CYS 56 (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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11C TYR* 3.6 22.9 - - + -
19C PHE* 4.2 13.9 - - - -
34C ALA* 3.1 4.1 - - - +
35C ILE* 2.7 55.5 + - + +
37C VAL* 4.4 8.3 - - - -
54C PHE* 4.5 3.4 - - - -
55C LEU* 1.3 73.3 - - - +
57C PRO* 1.3 64.2 - - - +
65C CYS* 2.0 47.3 - - - -
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Residues in contact with PRO 57 (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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11C TYR* 2.7 25.2 + - - -
32C ARG* 6.2 3.8 - - - -
33C VAL 5.0 0.2 - - - +
34C ALA* 4.0 9.6 - - + -
35C ILE* 6.3 0.2 - - - -
55C LEU 3.5 9.6 - - - +
56C CYS* 1.3 86.4 - - + +
58C TRP* 1.3 59.3 + - - +
59C ARG* 3.2 35.0 + - - +
65C CYS* 5.2 0.2 - - - -
66C PRO* 4.1 9.4 - - + -
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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