Contacts of the helix formed by residues 407 - 416 (chain B) in PDB entry 1B70
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 407 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405B PRO* 5.6 1.1 - - + -
406B PHE* 1.3 81.1 - - - +
408B PRO* 1.4 63.2 - - - +
409B GLU* 3.1 5.2 - - + +
410B TYR* 2.8 54.9 + - + +
411B ALA* 3.0 10.6 + - - +
413B ARG* 3.5 28.2 - - - +
440B PRO* 3.7 8.7 - - + +
441B THR* 4.0 19.1 - - - +
456B GLU* 2.7 36.8 + - - +
457B GLU* 5.6 0.4 + - - -
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Residues in contact with PRO 408 (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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406B PHE* 3.4 20.8 - - + +
407B ARG* 1.4 82.6 - - - +
409B GLU* 1.3 63.2 + - - +
411B ALA* 3.1 17.3 - - + +
412B ASN* 3.2 8.4 + - - -
421B GLU* 3.5 34.8 - - + +
424B GLN* 3.2 34.6 + - - +
425B ILE* 4.5 6.3 - - + -
440B PRO 3.3 17.3 - - - +
442B TYR* 3.8 15.0 - - + -
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Residues in contact with GLU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B ARG* 3.1 6.0 - - + +
408B PRO* 1.3 78.0 - - - +
410B TYR* 1.3 59.2 + - - +
412B ASN* 3.2 11.2 + - - +
413B ARG* 2.7 76.6 + - - +
440B PRO* 6.0 5.4 - - + +
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Residues in contact with TYR 410 (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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311A THR* 5.5 5.1 + - - -
407B ARG* 2.8 34.3 + - + +
409B GLU* 1.3 87.0 + - - +
411B ALA* 1.3 53.5 + - - +
413B ARG* 3.1 37.4 + - + +
414B LEU* 2.7 69.6 + - + +
456B GLU* 3.4 32.5 - - + -
457B GLU* 3.2 32.2 + - + +
460B VAL* 4.7 7.4 - - + -
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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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406B PHE* 3.9 14.8 - - + -
407B ARG 3.0 4.8 + - - +
408B PRO 3.1 13.7 + - - +
410B TYR* 1.3 78.1 - - - +
412B ASN* 1.3 57.4 + - - +
414B LEU* 3.0 4.4 + - - +
415B LEU* 3.0 37.2 + - + +
419B TYR* 6.2 0.4 - - + -
424B GLN* 3.4 20.4 - - - +
460B VAL* 3.9 25.4 - - + -
463B VAL* 5.5 3.8 - - + -
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Residues in contact with ASN 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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408B PRO 3.2 8.3 + - - -
409B GLU* 3.4 9.6 - - - +
411B ALA* 1.3 74.3 - - - +
413B ARG* 1.3 57.9 - - - +
415B LEU* 5.2 0.2 - - - -
416B GLY* 2.7 32.6 + - - -
417B THR* 2.9 37.2 + - - +
418B SER* 3.8 2.4 - - - +
419B TYR* 2.7 51.9 + - - +
424B GLN* 3.2 15.6 - - - +
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Residues in contact with ARG 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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227A GLY* 4.5 7.2 - - - +
228A ILE 4.3 3.1 - - - +
229A ALA* 3.4 15.1 - - - +
407B ARG* 3.5 28.5 - - - +
409B GLU* 2.7 55.7 + - - +
410B TYR* 3.1 43.0 - - + +
412B ASN* 1.3 76.0 - - - +
414B LEU* 1.3 62.2 + - - +
416B GLY* 3.9 1.2 + - - -
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Residues in contact with LEU 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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228A ILE 4.3 1.3 - - - +
229A ALA* 2.9 7.7 - - - +
230A MET* 2.9 20.4 + - - +
262A GLU 4.9 1.3 - - - +
263A PRO* 4.5 13.7 - - + -
285A MET* 3.5 31.9 - - + +
311A THR* 3.5 19.7 - - + +
410B TYR* 2.7 48.6 + - + +
411B ALA* 3.0 9.6 + - - +
413B ARG* 1.3 72.4 - - - +
415B LEU* 1.3 61.5 + - + +
457B GLU* 4.7 9.9 - - + -
460B VAL* 4.3 20.6 - - + -
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Residues in contact with LEU 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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229A ALA* 3.6 0.9 - - - -
230A MET* 3.1 19.1 + - + +
231A ALA 2.9 26.5 + - - -
263A PRO* 4.2 19.3 - - + -
411B ALA* 3.0 17.7 + - + +
414B LEU* 1.3 79.7 - - + +
416B GLY* 1.3 62.6 + - - +
417B THR* 3.5 20.4 - - + +
419B TYR* 3.7 29.8 - - + +
460B VAL* 3.9 22.7 - - + -
463B VAL* 5.2 2.5 - - + -
464B ALA* 4.1 24.7 - - + +
472B ILE* 3.7 11.9 - - + +
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Residues in contact with GLY 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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229A ALA* 3.6 13.2 - - - +
231A ALA* 4.1 7.9 - - - +
412B ASN 2.7 12.7 + - - -
413B ARG 4.3 1.6 - - - -
414B LEU 3.4 2.0 - - - -
415B LEU* 1.3 75.8 - - - +
417B THR* 1.3 60.2 + - - +
473B PRO* 3.0 28.2 - - - +
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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