Contacts of the helix formed by residues 410 - 420 (chain B) in PDB entry 2N97
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 ARG 410 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354B SER* 6.4 0.4 - - - -
355B ALA* 4.9 11.5 - - - +
358B THR* 3.5 29.0 - - + +
361B HIS* 5.9 1.6 - - + -
405B LEU* 3.0 26.2 + - + +
408B ILE* 3.6 31.6 - - + +
409B GLN* 1.3 83.5 + - - +
411B ALA* 1.3 58.0 + - - +
412B ASP* 3.1 32.9 + - - +
413B LEU* 3.0 36.4 + - + +
414B VAL* 3.4 7.3 + - - +
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Residues in contact with ALA 411 (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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405B LEU 4.0 3.0 + - - -
406B ARG* 5.2 12.3 - - + +
409B GLN* 3.6 4.8 + - - +
410B ARG* 1.3 74.6 - - - +
412B ASP* 1.3 55.5 + - - +
414B VAL* 3.3 16.3 + - + +
415B GLU* 2.9 29.5 + - - +
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Residues in contact with ASP 412 (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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409B GLN 5.2 4.3 - - - +
410B ARG* 3.1 25.3 + - - +
411B ALA* 1.3 77.1 + - - +
413B LEU* 1.3 56.6 + - - +
415B GLU* 3.4 7.9 + - - +
416B SER* 3.0 31.9 + - - -
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Residues in contact with LEU 413 (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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347B VAL* 6.0 0.7 - - + -
350B LEU* 3.9 29.6 - - + -
351B LEU* 4.3 14.4 - - + -
355B ALA 5.7 0.4 - - - +
358B THR* 3.5 37.9 - - + +
362B LEU* 6.0 1.1 - - + -
405B LEU* 4.1 19.1 - - + -
410B ARG* 3.0 25.4 + - + +
412B ASP* 1.3 73.7 - - - +
414B VAL* 1.3 59.6 + - - +
416B SER* 3.5 3.5 + - - -
417B LEU* 2.9 59.7 + - + +
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Residues in contact with VAL 414 (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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402B LEU* 3.6 31.6 - - + +
405B LEU* 3.7 38.1 - - + +
406B ARG* 5.1 0.9 - - + +
410B ARG 3.4 5.4 + - - +
411B ALA* 3.3 16.8 + - + +
413B LEU* 1.3 76.7 - - - +
415B GLU* 1.3 63.4 + - - +
417B LEU* 3.4 4.6 + - - +
418B CYS* 3.1 32.8 + - - -
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Residues in contact with GLU 415 (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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411B ALA 2.9 16.8 + - - +
412B ASP* 3.6 8.1 - - - +
413B LEU 3.4 0.2 - - - -
414B VAL* 1.3 77.6 - - - +
416B SER* 1.3 62.7 + - - +
418B CYS* 3.4 10.1 + - - +
419B SER* 3.1 31.7 + - - +
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Residues in contact with SER 416 (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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350B LEU* 4.0 25.2 - - - +
412B ASP 3.0 17.3 + - - -
413B LEU* 3.8 5.6 - - - -
414B VAL 3.4 0.2 - - - -
415B GLU* 1.3 75.9 - - - +
417B LEU* 1.3 57.6 + - - +
419B SER* 3.2 4.7 + - - +
420B GLU* 2.8 50.6 + - - +
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Residues in contact with LEU 417 (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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343B LYS* 3.2 32.0 + - - +
346B GLU* 4.8 4.9 - - + -
347B VAL* 3.9 38.8 - - + +
350B LEU* 3.5 19.7 - - + -
398B LEU* 6.2 4.5 - - + -
401B LEU* 6.0 6.1 - - + -
402B LEU* 6.3 2.2 - - + -
405B LEU* 4.6 15.0 - - + -
413B LEU* 2.9 41.7 + - + +
414B VAL* 3.4 5.1 + - - +
416B SER* 1.3 72.3 - - - +
418B CYS* 1.3 61.9 + - - +
420B GLU* 4.0 3.0 - - + -
421B SER* 3.4 8.1 + - - -
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Residues in contact with CYS 418 (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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402B LEU* 5.6 4.9 - - - -
414B VAL* 3.1 32.5 + - - +
415B GLU* 3.7 11.7 - - - +
416B SER 3.3 0.2 - - - -
417B LEU* 1.3 75.7 - - - +
419B SER* 1.3 63.5 + - - +
421B SER* 3.2 21.5 - - - -
422B THR 4.7 0.5 + - - -
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Residues in contact with SER 419 (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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415B GLU* 3.1 23.9 + - - +
416B SER* 3.7 5.4 - - - -
418B CYS* 1.3 75.7 - - - +
420B GLU* 1.3 70.1 + - - +
421B SER 3.3 3.5 + - - -
422B THR* 3.8 15.8 + - - -
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Residues in contact with GLU 420 (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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343B LYS* 4.6 4.5 - - - +
346B GLU* 3.8 42.0 - - + +
350B LEU* 4.9 10.6 - - + +
416B SER* 2.8 41.1 + - - +
417B LEU* 4.0 6.7 - - + +
419B SER* 1.3 80.7 - - - +
421B SER* 1.3 60.8 + - - +
422B THR* 3.2 13.0 + - - +
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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