Contacts of the helix formed by residues 404 - 417 (chain B) in PDB entry 1D8D
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 GLY 404 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B HIS* 4.5 0.4 - - - -
112B GLU* 3.1 29.1 + - - -
396B PRO 3.9 8.5 - - - -
403B ILE* 1.3 74.7 - - - +
405B PRO* 1.4 65.9 - - - +
406B ASP* 3.1 12.1 - - - -
407B LYS* 2.8 23.1 + - - +
408B VAL* 3.0 10.4 + - - +
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Residues in contact with PRO 405 (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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396B PRO* 3.4 36.3 - - + +
397B THR 4.0 5.6 - - - +
398B HIS* 3.8 37.6 - - + +
403B ILE 3.4 0.2 - - - -
404B GLY* 1.4 82.7 - - - +
406B ASP* 1.3 63.8 + - - +
408B VAL* 3.4 2.2 + - + +
409B ILE* 3.1 36.5 + - + +
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Residues in contact with ASP 406 (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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112B GLU* 4.8 0.7 - - - +
396B PRO* 6.1 0.2 - - - +
404B GLY* 3.4 16.1 - - - -
405B PRO* 1.3 80.7 - - - +
407B LYS* 1.3 85.1 + - - +
409B ILE* 3.5 8.3 + - - +
410B GLN* 2.8 36.8 + - - +
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Residues in contact with LYS 407 (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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112B GLU* 3.4 28.6 + - - +
118B ILE* 6.3 0.6 - - - +
161B CYS 3.4 27.2 - - - +
162B ILE* 2.9 25.4 + - - +
163B ILE 4.8 5.1 + - - -
164B GLY* 4.9 4.7 - - - -
169B TYR* 4.6 0.2 + - - -
403B ILE* 4.0 13.9 - - + -
404B GLY 2.8 9.3 + - - +
406B ASP* 1.3 91.4 + - - +
408B VAL* 1.3 60.2 + - - +
410B GLN* 3.8 17.7 - - - +
411B ALA* 2.9 32.6 + - - +
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Residues in contact with VAL 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LEU* 4.4 5.2 - - + -
398B HIS* 3.7 34.1 - - + +
401B TYR* 3.7 31.2 - - + -
403B ILE* 3.5 30.5 - - + -
404B GLY 3.0 7.3 + - - +
405B PRO 3.5 7.0 - - - +
406B ASP 3.3 0.2 - - - -
407B LYS* 1.3 78.2 - - - +
409B ILE* 1.3 66.9 + - + +
411B ALA* 3.7 0.7 - - - +
412B THR* 2.9 39.8 + - + +
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Residues in contact with ILE 409 (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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398B HIS* 6.3 1.3 - - + -
405B PRO* 3.1 21.7 + - + +
406B ASP* 3.8 7.4 - - - +
408B VAL* 1.3 77.8 - - + +
410B GLN* 1.3 65.3 + - - +
412B THR* 3.3 7.6 + - - +
413B THR* 3.0 37.8 + - - +
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Residues in contact with GLN 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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164B GLY* 3.1 29.2 - - - +
169B TYR* 3.3 12.7 + - + +
406B ASP* 2.8 23.1 + - - +
407B LYS* 3.8 19.0 - - - +
409B ILE* 1.3 78.9 - - - +
411B ALA* 1.3 62.5 + - - +
413B THR* 3.8 4.4 - - - +
414B HIS* 3.0 24.3 + - - +
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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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161B CYS* 3.6 31.0 - - + -
169B TYR* 3.4 19.4 + - + -
213B LEU* 4.2 9.0 - - + +
407B LYS 2.9 18.6 + - - +
408B VAL 3.7 3.1 - - - +
410B GLN* 1.3 75.1 - - - +
412B THR* 1.3 65.7 + - - +
414B HIS* 3.2 2.6 + - - +
415B PHE* 3.0 34.0 + - + -
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Residues in contact with THR 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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212B SER 4.7 5.4 - - - +
213B LEU* 3.9 35.0 - - + +
215B ASN* 6.5 0.2 - - - -
401B TYR* 5.3 3.4 - - - +
408B VAL* 2.9 23.4 + - + +
409B ILE* 3.3 13.0 + - - +
411B ALA* 1.3 74.2 - - - +
413B THR* 1.3 67.8 + - - +
415B PHE* 3.2 2.1 + - - +
416B LEU* 2.8 39.8 + - - +
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Residues in contact with THR 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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409B ILE* 3.0 30.3 + - - +
410B GLN* 3.8 5.4 - - - -
412B THR* 1.3 78.4 + - - +
414B HIS* 1.3 66.0 + - - +
416B LEU* 3.3 16.9 + - - +
417B GLN* 3.4 21.1 + - + +
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Residues in contact with HIS 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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166B GLU* 3.4 35.6 + - - -
169B TYR* 3.6 45.5 - + + +
170B ASN* 4.7 2.8 + - - -
410B GLN 3.0 18.5 + - - +
411B ALA 3.2 2.9 + - - +
413B THR* 1.3 78.6 - - - +
415B PHE* 1.3 77.4 + + - +
417B GLN* 3.2 42.9 + - - +
418B LYS* 3.7 29.4 + - - +
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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
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161B CYS* 4.8 3.8 - - - -
169B TYR* 3.7 55.2 - + + -
172B ILE* 4.1 14.1 - - + -
174B ARG* 3.7 34.5 + - + -
213B LEU 3.2 25.1 - - - +
214B THR* 3.6 22.2 - - + +
215B ASN* 3.1 17.0 + - + +
411B ALA* 3.0 30.4 + - + +
412B THR 4.0 1.6 - - - +
414B HIS* 1.3 87.0 - + - +
416B LEU* 1.3 56.5 + - - +
417B GLN 3.0 5.8 - - - -
418B LYS* 3.1 26.9 + - + +
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Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ASN* 3.7 29.5 + - + +
412B THR* 2.8 31.4 + - - +
413B THR* 3.7 9.9 - - - +
414B HIS 3.3 0.6 - - - -
415B PHE* 1.3 74.2 - - - +
417B GLN* 1.3 60.7 + - - +
418B LYS 3.1 7.9 - - - +
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Residues in contact with GLN 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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413B THR* 3.4 18.6 + - + +
414B HIS* 3.2 38.4 + - - +
416B LEU* 1.3 77.8 - - - +
418B LYS* 1.3 72.3 + - - +
419B PRO* 4.5 1.4 - - - +
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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