Contacts of the strand formed by residues 410 - 414 (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 LEU 410 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368R ALA* 3.8 22.9 - - + -
378R LEU* 3.8 28.7 - - + -
380R ILE* 4.5 7.2 - - + -
401R MET* 3.4 27.8 - - + -
402R VAL 3.4 22.0 - - - +
403R TRP* 3.9 27.4 - - + +
409R GLU* 1.3 73.4 - - - +
411R VAL* 1.3 67.0 + - - +
412R THR* 4.1 2.9 - - + -
423R LEU* 3.4 2.6 - - - +
424R TRP* 2.6 48.1 + - + -
426R CYS* 3.5 11.8 - - - -
429R MET* 5.3 0.7 - - + -
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Residues in contact with VAL 411 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401R MET* 3.3 5.2 - - - +
402R VAL* 2.9 46.3 + - + +
409R GLU 5.3 0.4 - - - +
410R LEU* 1.3 79.4 - - - +
412R THR* 1.3 66.2 + - - +
421R LEU* 4.1 29.4 - - + -
422R THR 3.2 10.1 - - - +
423R LEU* 3.7 21.8 - - + -
435R LEU* 5.7 0.7 - - + -
445R LEU* 3.9 6.8 - - + +
454R VAL* 4.6 11.0 - - + -
468R LEU* 4.1 12.6 - - + -
469R PHE* 3.8 20.0 - - + -
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Residues in contact with THR 412 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378R LEU* 4.4 12.1 - - + -
394R SER* 6.5 0.2 - - - -
398R ILE* 4.3 9.9 - - + -
400R ASN 3.6 4.7 - - - -
401R MET* 4.1 28.9 - - + -
410R LEU* 4.1 2.4 - - + -
411R VAL* 1.3 78.2 - - - +
413R SER* 1.3 59.8 + - - +
414R HIS* 2.9 29.5 + - + -
421R LEU* 3.2 4.9 - - - +
422R THR* 2.8 35.2 + - - -
424R TRP* 2.9 30.3 + - + +
445R LEU* 4.7 0.2 - - - -
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Residues in contact with SER 413 (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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398R ILE* 3.9 1.9 - - - -
399R CYS* 2.9 26.2 + - - -
400R ASN* 3.1 30.1 + - - +
412R THR* 1.3 75.1 - - - +
414R HIS* 1.3 61.4 + - - +
420R ASN 3.5 4.3 - - - -
421R LEU* 4.0 5.6 - - - +
442R VAL* 2.8 40.7 + - - -
445R LEU* 3.8 15.1 - - - +
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Residues in contact with HIS 414 (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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394R SER* 3.3 32.5 - - - -
396R SER* 2.8 25.4 + - - +
397R GLN 3.3 9.7 + - - -
398R ILE* 3.8 11.6 - - + +
399R CYS* 4.0 3.6 - - - -
412R THR* 2.9 32.5 + - - -
413R SER* 1.3 79.2 - - - +
415R GLY* 1.3 61.6 + - - +
418R LYS* 3.0 25.0 - - + +
419R TYR* 3.7 7.3 - - - -
420R ASN* 2.7 20.6 + - + +
422R THR* 3.5 23.4 + - + +
442R VAL* 3.0 21.4 + - - +
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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