Contacts of the helix formed by residues 12 - 17 (chain F) 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 SER 12 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F VAL 3.2 7.2 + - - +
11F SER* 1.3 76.8 - - - +
13F CYS* 1.3 66.2 + - - +
14F GLN* 4.2 7.7 - - - +
15F GLN* 3.0 34.3 + - - +
16F CYS* 3.2 15.2 + - - +
25F TRP* 3.4 19.6 - - - -
439F ALA* 5.2 13.0 - - - +
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Residues in contact with CYS 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F SER* 1.3 73.9 - - - +
14F GLN* 1.3 61.5 + - + +
16F CYS* 3.6 7.1 - - - +
17F LEU* 3.3 12.6 - - - +
25F TRP* 3.5 55.0 - - + +
55F GLU* 3.6 11.4 - - - -
435F CYS* 2.1 58.1 - - + -
436F ALA 4.8 0.2 - - - -
438F GLN* 3.7 24.0 + - - +
439F ALA* 5.1 0.2 - - - +
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Residues in contact with GLN 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F SER* 3.1 6.7 - - - +
13F CYS* 1.3 79.9 - - - +
15F GLN* 1.3 59.6 + - - +
16F CYS 3.6 0.3 + - - -
17F LEU* 3.8 9.3 + - - +
18F ALA* 3.9 9.0 + - - +
433F CYS 3.8 19.4 - - - +
434F ASP* 2.9 41.4 + - - +
435F CYS* 4.0 9.6 - - - -
436F ALA 5.2 0.2 - - - +
437F CYS* 4.5 13.7 + - - +
438F GLN 4.1 16.7 + - - +
439F ALA* 5.4 4.0 - - - +
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Residues in contact with GLN 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F VAL* 2.9 51.8 - - - +
12F SER* 3.0 22.6 + - - +
14F GLN* 1.3 76.1 - - - +
16F CYS* 1.3 64.5 + - - +
17F LEU 3.4 0.2 - - - -
18F ALA* 3.3 22.1 + - + +
19F VAL* 3.8 11.3 - - + +
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Residues in contact with CYS 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F VAL 5.1 3.8 + - - +
12F SER 3.2 17.4 + - - +
13F CYS 3.6 7.0 - - - +
15F GLN* 1.3 74.0 - - - +
17F LEU* 1.3 63.3 + - + +
18F ALA 3.0 5.3 + - - -
19F VAL* 3.1 21.7 + - - +
23F CYS* 3.7 13.5 - - - +
24F ALA 2.7 31.2 - - - +
25F TRP* 3.9 5.2 - - + -
38F CYS* 2.0 50.3 - - + -
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Residues in contact with LEU 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F CYS* 3.3 14.4 - - - +
14F GLN 4.0 6.5 - - - +
15F GLN 3.4 0.2 - - - -
16F CYS* 1.3 76.7 - - + +
18F ALA* 1.3 56.9 + - - +
19F VAL 3.1 4.3 + - - -
20F SER 3.7 6.1 + - - -
23F CYS* 4.1 9.4 - - - +
24F ALA* 4.8 7.0 - - - -
55F GLU 4.0 9.4 - - - +
57F PRO* 3.5 43.5 - - + -
93F ARG* 3.0 33.6 + - - +
94F PRO* 3.4 20.7 - - + +
432F ASP 5.1 2.2 - - - +
433F CYS 4.6 1.8 - - - +
434F ASP* 3.8 22.0 - - - +
435F CYS* 3.6 20.6 - - - -
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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