Contacts of the strand formed by residues 420 - 425 (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 SER 420 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E GLY 3.2 24.5 + - - -
21E PHE* 3.5 12.8 - - - -
22E SER* 3.5 7.7 - - - -
23E LEU* 2.9 29.9 + - - +
418E GLY 3.5 5.6 - - - +
419E PHE* 1.3 79.6 - - - +
421E LEU* 1.3 61.4 + - - +
437E VAL* 3.7 3.1 - - - -
438E GLY* 2.9 30.1 + - - -
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Residues in contact with LEU 421 (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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23E LEU* 3.9 3.3 - - - +
359E ALA* 3.8 24.2 - - + +
360E ILE 5.2 0.6 - - - -
361E ALA* 3.5 22.5 - - + +
375E ALA* 3.8 27.1 - - + +
376E VAL 4.2 1.1 - - - -
377E ALA* 3.9 12.3 - - + +
389E VAL* 4.0 17.0 - - + -
418E GLY 3.6 13.5 - - - +
419E PHE 4.3 0.4 + - - -
420E SER* 1.3 79.7 + - - +
422E ARG* 1.3 75.7 + - - +
435E LEU* 4.4 6.3 - - + -
436E ILE 3.8 3.8 - - - +
437E VAL* 3.8 31.6 - - + -
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Residues in contact with ARG 422 (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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22E SER* 6.2 0.4 - - - -
23E LEU* 3.0 31.7 + - + +
24E ASP* 3.6 35.2 + - - +
25E PHE* 3.7 17.8 - - + -
97E VAL 4.3 10.3 + - - -
98E VAL* 5.4 4.0 - - - +
361E ALA* 3.9 5.6 - - - +
362E PRO* 6.4 1.6 - - - -
421E LEU* 1.3 83.2 + - - +
423E GLY* 1.3 66.0 + - - +
435E LEU* 3.3 9.0 - - - +
436E ILE* 2.8 51.4 + - + +
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Residues in contact with GLY 423 (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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25E PHE* 3.6 14.5 - - - -
361E ALA* 4.4 5.7 - - - +
362E PRO 4.0 5.3 + - - +
363E LEU* 4.4 11.2 - - - -
422E ARG* 1.3 83.0 - - - +
424E ALA* 1.3 70.2 + - - +
425E VAL* 3.3 5.7 + - - +
434E ASP 3.2 15.7 - - - -
435E LEU* 4.4 1.3 - - - -
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Residues in contact with ALA 424 (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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362E PRO* 3.2 18.6 - - + +
363E LEU* 3.8 9.4 - - - +
364E GLY* 3.6 24.6 - - - +
423E GLY* 1.3 73.9 - - - +
425E VAL* 1.3 64.0 + - + +
433E PRO* 4.2 9.7 - - - +
434E ASP 3.6 5.1 + - - -
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Residues in contact with VAL 425 (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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25E PHE* 3.6 49.8 - - + -
33E VAL* 4.1 16.6 - - + -
423E GLY 3.3 2.8 - - - +
424E ALA* 1.3 85.5 - - - +
426E ASP* 1.3 69.6 + - - +
427E ILE 3.2 6.1 + - - -
433E PRO* 4.1 3.1 - - - -
434E ASP* 2.9 27.3 + - - +
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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