Contacts of the strand formed by residues 473 - 477 (chain B) in PDB entry 1E8U
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 PRO 473 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405B LEU* 4.4 6.1 - - - +
414B TYR* 3.3 27.3 - - + +
424B ALA* 4.3 11.4 - - + -
425B LEU 4.6 1.3 - - - +
426B LEU* 3.7 28.8 - - + +
444B PHE* 5.0 2.0 - - + -
447B PHE* 3.6 21.3 - - + -
471B THR 4.0 2.2 - - - +
472B ASP* 1.3 90.9 - - + +
474B TYR* 1.3 61.2 + - - +
475B PRO* 3.7 7.3 - - - +
487B VAL* 3.6 21.1 - - + -
488B PHE 3.5 5.8 - - - +
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Residues in contact with TYR 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLY* 4.1 19.1 + - - -
138B LYS 5.0 1.4 + - - -
140B LEU* 4.6 4.7 - - + -
403B ARG* 4.2 5.8 - - - -
405B LEU* 3.7 26.7 - - + -
406B THR 4.6 2.9 + - - -
407B VAL* 3.9 20.2 - - + +
472B ASP 4.1 0.4 + - - -
473B PRO* 1.3 73.0 - - - +
475B PRO* 1.3 92.8 - - - +
476B LEU* 3.0 2.5 + - - +
487B VAL* 3.2 2.7 - - - -
488B PHE* 2.8 35.9 + - - +
529B SER 3.5 29.4 - - - +
530B THR* 3.7 16.1 - - + +
531B CYS* 3.4 53.0 + - + -
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Residues in contact with PRO 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LYS 5.3 0.2 - - - +
140B LEU* 5.2 1.7 + - - +
405B LEU* 3.7 17.5 - - + -
407B VAL* 3.7 18.9 - - + +
412B PHE* 3.7 27.8 - - + -
426B LEU* 3.8 16.4 - - + -
473B PRO 3.7 7.9 - - - +
474B TYR* 1.3 103.1 - - + +
476B LEU* 1.3 59.6 + - - +
478B PHE* 3.5 24.2 - - + -
484B LEU* 3.7 7.2 - - + -
487B VAL* 3.7 10.3 - - + -
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Residues in contact with LEU 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU* 3.5 35.8 + - + -
141B ILE* 3.0 31.5 + - + +
474B TYR 3.0 8.4 + - - +
475B PRO* 1.3 74.6 - - - +
477B ILE* 1.3 73.0 + - + +
478B PHE* 3.6 9.2 - - - -
486B GLY 2.8 13.6 + - - +
487B VAL* 4.2 4.0 - - - -
488B PHE* 4.3 15.7 - - + +
505B VAL* 4.4 12.8 - - + -
531B CYS* 4.2 10.8 - - + -
540B THR* 4.1 12.3 - - + -
542B CYS* 4.5 0.2 - - - -
565B ILE* 4.1 30.5 - - + -
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Residues in contact with ILE 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ILE* 3.0 28.5 - - + +
143B ASP* 4.3 12.3 - - + +
148B VAL* 3.7 28.0 - - + +
151B PHE* 3.5 34.5 - - + -
476B LEU* 1.3 84.8 - - + +
478B PHE* 1.3 63.1 + - - +
484B LEU* 3.5 3.6 - - - +
485B ARG* 2.6 48.2 + - + +
486B GLY* 2.8 24.4 + - - +
505B VAL* 4.2 11.7 - - + -
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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