Contacts of the strand formed by residues 424 - 429 (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 ALA 424 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414B TYR* 4.8 7.2 - - + -
422B SER 3.5 1.3 + - - -
423B PRO* 1.3 71.4 - - - +
425B LEU* 1.3 59.7 + - - +
443B THR* 3.4 7.6 - - - -
444B PHE* 3.3 30.4 + - + -
447B PHE* 2.9 49.7 + - + +
471B THR 5.1 0.7 - - - +
473B PRO* 4.3 18.8 - - + -
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B TYR* 4.6 4.9 - - + -
397B LEU* 3.6 27.6 - - + -
413B LEU 4.6 0.4 - - - -
414B TYR* 3.2 33.9 - - - -
415B GLN* 3.6 31.8 + - - +
416B ARG 5.4 1.8 - - - +
417B GLY* 5.6 4.0 - - - -
421B PHE* 3.6 35.7 - - + +
423B PRO 3.3 2.0 + - - +
424B ALA* 1.3 73.6 - - - +
426B LEU* 1.3 61.7 + - - +
427B TYR* 4.0 12.6 - - + +
441B PRO* 3.5 32.3 - - + -
442B TYR 3.6 0.7 - - - -
443B THR* 3.8 6.3 - - + -
473B PRO* 4.6 1.5 - - - +
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Residues in contact with LEU 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B LEU* 4.8 3.6 - - + -
412B PHE* 3.9 21.0 - - + -
413B LEU 3.8 0.4 - - - -
414B TYR* 3.9 22.0 - - + +
424B ALA 4.2 0.2 + - - -
425B LEU* 1.3 79.9 - - - +
427B TYR* 1.3 63.3 + - - +
428B PRO* 3.3 4.5 - - - +
441B PRO* 4.0 0.9 - - - +
442B TYR* 2.8 48.2 + - + +
444B PHE* 4.3 5.4 - - + -
473B PRO* 3.7 25.6 - - + +
475B PRO* 3.8 18.6 - - + -
484B LEU* 3.5 29.2 - - + -
487B VAL* 4.1 12.6 - - + -
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Residues in contact with TYR 427 (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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337B TYR* 4.1 1.1 - - - -
395B VAL* 3.2 29.3 + - + -
396B THR* 3.4 10.0 - - + -
397B LEU* 3.1 26.3 + - - +
412B PHE* 3.5 2.1 - - - -
413B LEU* 2.9 58.9 + - + +
415B GLN* 2.8 42.0 + - + -
425B LEU* 4.0 12.2 - - + +
426B LEU* 1.3 69.8 - - - +
428B PRO* 1.3 71.5 - - - +
429B MET 3.2 0.3 + - - -
438B LEU* 4.0 22.4 - - + -
439B HIS 3.5 15.0 - - - +
441B PRO* 3.4 26.7 - - + -
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Residues in contact with PRO 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B HIS 3.7 7.9 - - - +
412B PHE* 4.4 5.6 - - + -
426B LEU 3.3 7.0 - - - +
427B TYR* 1.3 83.9 - - - +
429B MET* 1.3 58.7 + - - +
430B THR* 6.2 0.7 - - + -
438B LEU* 3.3 4.5 - - - -
439B HIS* 3.0 48.9 + - + +
440B SER 3.1 27.4 - - - +
441B PRO* 3.8 0.2 - - + -
442B TYR* 3.7 26.2 - - + -
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Residues in contact with MET 429 (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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308B ILE* 4.0 13.7 - - + -
313B TRP* 4.2 13.9 - - + -
373B ILE* 3.8 22.4 - - - -
404B ILE* 3.9 37.9 - - + -
411B HIS* 2.9 46.7 + - + +
412B PHE 4.4 3.4 - - - +
413B LEU* 4.7 2.2 - - - -
427B TYR 3.2 3.1 + - - +
428B PRO* 1.3 75.4 - - - +
430B THR* 1.3 65.9 + - - +
431B VAL* 3.8 25.4 - - + -
436B ALA* 4.0 11.0 - - + -
437B THR 3.3 5.6 - - - +
438B LEU* 3.6 17.9 - - + -
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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