Contacts of the strand formed by residues 387 - 391 (chain B) in PDB entry 3EI1
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 LEU 387 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B GLN* 3.7 18.2 - - + +
130B PHE* 4.0 32.8 - - + -
131B ILE* 4.1 23.3 - - + -
134B LEU* 5.0 0.7 - - + -
381B TRP* 3.5 9.5 - - - -
382B HIS* 3.0 34.4 + - + -
385B TYR* 2.8 23.1 + - + -
386B ASP* 1.3 81.9 - - - +
388B ILE* 1.3 62.4 + - - +
408B ILE* 4.3 15.7 - - + -
409B TYR 3.3 14.8 - - - +
410B ASP* 3.9 10.8 - - + +
417B VAL* 4.6 5.2 - - + -
434B PHE* 5.9 2.5 - - + -
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Residues in contact with ILE 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 3.6 33.7 - - + -
349B ILE* 4.5 5.8 - - + -
351B VAL* 3.9 16.8 - - + -
364B ILE* 4.0 18.4 - - + -
379B ALA* 3.8 27.1 - - + -
380B THR 3.4 5.6 - - - +
381B TRP* 4.4 7.4 - - + -
387B LEU* 1.3 78.3 - - - +
389B VAL* 1.3 64.4 + - - +
390B ALA* 4.6 3.8 - - + +
407B ASP 3.3 1.0 - - - +
408B ILE* 3.0 11.9 - - - +
409B TYR* 2.8 46.3 + - + +
411B ALA* 4.0 18.6 - - + +
434B PHE* 5.6 0.9 - - - -
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Residues in contact with VAL 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LYS 4.2 1.4 - - - +
379B ALA* 3.2 4.7 - - - +
380B THR* 2.9 63.7 + - - +
381B TRP 4.6 0.7 - - - +
388B ILE* 1.3 72.1 - - - +
390B ALA* 1.3 60.3 + - - +
406B ILE* 4.0 12.3 - - + -
407B ASP 3.3 3.1 - - - +
408B ILE* 3.7 20.4 - - + -
432B ASN* 4.1 13.6 - - + +
434B PHE* 3.6 42.2 - - + -
441B LEU* 3.8 16.6 - - + -
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Residues in contact with ALA 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B THR* 6.3 0.2 - - + -
349B ILE* 3.6 30.5 - - + -
366B HIS* 3.8 13.5 + - + +
377B ILE* 5.1 3.1 - - + -
378B LYS 4.8 2.2 - - - -
379B ALA* 3.8 12.6 - - + +
388B ILE* 4.2 2.2 - - + -
389B VAL* 1.3 76.2 - - - +
391B GLY* 1.3 61.1 + - - +
406B ILE* 4.4 0.4 - - - -
407B ASP* 2.8 42.8 + - + +
409B TYR* 5.1 1.3 - - + -
432B ASN* 4.1 5.2 - - - +
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Residues in contact with GLY 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B HIS* 3.1 14.5 - - - -
377B ILE* 3.3 27.3 - - - +
378B LYS 5.3 0.4 + - - -
390B ALA* 1.3 72.5 - - - +
392B ARG* 1.3 59.2 + - - -
405B THR 3.9 6.5 - - - -
406B ILE* 4.4 1.6 - - - -
429B ILE* 3.2 27.1 + - - -
430B SER 5.1 0.4 + - - -
432B ASN* 3.5 13.1 - - - +
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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
------------------------------------------------------------
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