Contacts of the strand formed by residues 410 - 415 (chain B) in PDB entry 2I91
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 SER 410 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B PHE* 3.2 23.8 - - - -
373B LEU* 4.2 15.3 - - - -
403B VAL 5.0 0.2 - - - -
404B ALA* 3.5 18.5 + - - +
407B GLU* 2.6 24.3 + - - -
408B LYS 2.7 13.0 + - - +
409B ASP* 1.3 75.3 - - - +
411B HIS* 1.3 59.6 + - - +
412B MET* 4.1 4.4 + - - +
426B VAL* 5.4 7.3 - - - +
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Residues in contact with HIS 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B PHE 3.1 7.7 + - - +
372B LEU* 3.4 18.7 - - + +
373B LEU* 3.0 22.6 + - - -
410B SER* 1.3 73.2 - - - +
412B MET* 1.3 78.1 + - - +
413B VAL* 3.4 18.4 - - + +
422B CYS* 5.9 0.9 - - + -
453B TRP* 4.0 21.5 - + + -
459B THR* 5.6 6.7 - - + -
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Residues in contact with MET 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B LEU* 3.3 11.7 - - + +
375B ILE* 5.7 0.4 - - + -
400B CYS* 3.8 28.9 - - - +
401B MET* 4.5 13.0 - - - +
404B ALA* 4.1 24.9 - - + -
410B SER 5.0 2.9 - - - +
411B HIS* 1.3 82.6 + - - +
413B VAL* 1.3 72.0 + - - +
422B CYS* 3.6 21.3 - - - +
424B ILE* 3.6 28.0 - - + +
425B THR* 3.6 3.8 - - - -
426B VAL* 3.6 36.6 - - + +
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Residues in contact with VAL 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 3.8 15.0 - - + -
373B LEU 2.7 9.4 + - - +
374B ALA* 3.1 27.3 - - + -
375B ILE* 2.7 34.8 + - - +
411B HIS* 3.4 22.4 - - + +
412B MET* 1.3 82.7 - - - +
414B ALA* 1.3 55.2 + - - +
415B PHE* 5.5 0.2 - - + -
419B MET* 4.0 25.6 - - + -
420B LEU 5.4 1.6 - - - +
422B CYS* 4.1 9.2 - - + -
450B PRO* 5.1 1.8 - - + -
453B TRP* 4.3 18.2 - - + -
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Residues in contact with ALA 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ILE* 3.3 15.3 - - + +
377B VAL* 3.9 17.3 - - + -
413B VAL* 1.3 75.4 - - - +
415B PHE* 1.3 64.9 + - - +
419B MET* 4.1 6.4 - - - +
420B LEU* 3.2 33.2 + - + +
422B CYS* 4.4 3.2 - - - +
423B PRO* 4.1 14.6 - - + -
437B MET* 5.6 1.3 - - + -
440B ILE* 4.1 17.0 - - + -
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Residues in contact with PHE 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ALA* 3.9 15.0 - - + -
375B ILE 3.0 13.0 + - - -
376B ASP* 3.5 31.7 - - + +
377B VAL* 2.7 35.9 + - - +
378B SER 3.8 0.2 + - - -
413B VAL* 5.5 0.2 - - + -
414B ALA* 1.3 78.0 - - - +
416B SER* 1.3 71.3 + - - +
418B GLU 3.5 12.8 - - - +
419B MET* 4.2 15.0 - - - -
420B LEU* 4.3 1.6 - - - -
445B THR* 4.7 0.2 - - + -
446B ASP 3.5 24.5 - - - -
447B CYS* 3.7 22.0 - - - -
449B LEU* 4.2 3.4 - - + -
450B PRO* 3.7 28.5 - - + -
466B VAL* 3.8 22.4 - - + -
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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