Contacts of the strand formed by residues 398 - 403 (chain R) in PDB entry 5A31
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 ILE 398 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188R PHE* 3.6 16.8 - - - -
356R ALA* 3.7 23.9 + - + +
370R GLY* 3.7 16.9 - - - +
371R GLY 2.8 23.1 + - - +
376R ARG 3.6 3.6 - - - +
377R ARG 3.3 35.7 - - - +
378R LEU* 3.9 11.0 - - + +
394R SER* 3.4 26.0 - - - +
396R SER 3.8 1.3 - - - +
397R GLN* 1.3 70.7 - - - +
399R CYS* 1.3 61.4 + - - +
400R ASN 3.8 10.3 - - - +
401R MET* 4.4 3.8 - - + -
412R THR* 4.3 12.6 - - + -
413R SER 3.9 4.9 - - - +
414R HIS* 3.8 9.4 - - + -
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Residues in contact with CYS 399 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188R PHE* 3.6 30.1 - - + -
355R LYS* 2.9 36.4 + - - +
356R ALA* 4.0 4.0 - - - -
397R GLN* 3.7 8.3 - - - -
398R ILE* 1.3 72.8 - - - +
400R ASN* 1.3 59.7 + - - +
413R SER 2.9 7.8 + - - +
414R HIS 4.0 0.7 - - - -
415R GLY* 3.4 33.4 - - - -
442R VAL 3.6 18.4 - - - +
443R LEU* 3.6 22.2 - - + -
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Residues in contact with ASN 400 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191R SER* 3.4 27.6 + - - -
316R LYS* 5.1 5.2 + - - -
355R LYS* 3.8 6.0 - - - +
356R ALA* 3.5 15.9 - - - +
398R ILE* 3.8 3.5 - - - +
399R CYS* 1.3 74.6 - - - +
401R MET* 1.3 84.6 + - - +
412R THR* 3.6 2.9 - - - -
413R SER* 3.1 40.9 + - - +
443R LEU 2.8 25.2 + - - +
445R LEU* 3.8 24.7 + - + +
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Residues in contact with MET 401 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316R LYS* 4.1 14.0 + - - -
356R ALA* 3.6 28.7 - - + +
357R MET* 3.8 6.1 - - - +
358R ALA* 3.7 19.7 - - + +
368R ALA* 3.5 27.6 - - - -
369R THR 3.7 0.9 - - - -
370R GLY* 3.6 19.5 - - - +
378R LEU* 3.7 22.9 - - + -
398R ILE* 4.4 1.6 - - + -
400R ASN* 1.3 91.5 + - - +
402R VAL* 1.3 72.5 + - - +
410R LEU* 3.4 18.2 - - + -
411R VAL 3.3 9.0 - - - +
412R THR* 4.1 10.1 - - + -
445R LEU* 3.6 4.8 - - - +
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Residues in contact with VAL 402 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316R LYS* 5.6 3.4 - - - +
358R ALA* 4.6 2.2 - - - -
401R MET* 1.3 81.8 - - - +
403R TRP* 1.4 63.5 + - - +
404R SER 3.8 0.8 + - - +
410R LEU* 3.7 3.8 - - - -
411R VAL* 2.9 43.1 + - + +
445R LEU* 4.3 11.0 - - + +
446R THR* 4.3 10.3 - - - +
447R LEU* 3.8 52.3 - - + +
454R VAL* 4.7 9.9 - - + -
469R PHE* 5.8 0.4 - - + -
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Residues in contact with TRP 403 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358R ALA* 3.6 31.6 + - + +
359R TRP 3.5 26.5 - - - +
360R SER* 3.8 24.4 - - - +
361R PRO* 3.7 8.4 - - + +
362R HIS* 3.9 14.6 - + - -
366R VAL* 4.8 10.6 + - + +
367R LEU 5.2 0.6 - - - -
368R ALA* 3.8 17.6 - - + +
380R ILE* 5.2 8.1 - - + -
402R VAL* 1.4 70.6 - - - +
404R SER* 1.3 65.8 + - - +
405R LYS* 3.4 2.9 + - - +
408R ASN* 3.1 36.6 - - - -
409R GLU 3.4 17.5 - - - -
410R LEU* 3.9 16.7 - - + +
426R CYS* 3.3 33.9 - - + -
447R LEU* 3.7 12.0 - - - +
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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