Contacts of the helix formed by residues 357 - 361 (chain B) in PDB entry 4DTZ
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 ILE 357 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B PRO* 3.6 11.2 - - + -
328B ALA 3.4 25.4 - - - +
329B PRO 2.9 19.1 + - - +
330B ALA 4.0 0.2 - - - +
331B PHE* 3.8 31.4 - - + -
355B VAL* 4.1 9.2 - - + +
356B LEU* 1.3 72.0 - - - +
358B PRO* 1.4 65.9 - - + +
359B GLN 3.1 0.2 + - - -
360B LEU* 3.2 9.7 + - + +
361B HIS* 3.0 53.8 + - + +
391B LYS* 3.5 23.8 - - + +
392B PRO* 4.6 2.9 - - + -
500B HEM 4.4 6.3 - - + -
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Residues in contact with PRO 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 4.2 4.5 - - + -
30B MET* 3.6 33.2 - - + -
324B LEU 4.5 1.1 - - - +
325B TRP* 4.6 6.3 - - + -
326B PRO* 3.7 24.5 - - + +
329B PRO* 3.2 26.5 - - + +
356B LEU* 3.6 11.2 - - + -
357B ILE* 1.4 90.6 - - + +
359B GLN* 1.3 59.3 + - - +
361B HIS* 3.6 2.3 + - + +
362B ARG* 2.9 41.5 + - - +
439B LEU* 4.9 0.4 - - + -
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Residues in contact with GLN 359 (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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30B MET* 3.4 43.6 + - + +
33B ALA* 3.7 12.1 - - + +
34B ASP* 3.1 25.4 + - - +
53B SER* 3.4 30.0 + - - +
356B LEU* 3.0 32.7 + - + +
358B PRO* 1.3 76.9 - - - +
360B LEU* 1.3 66.4 + - - +
361B HIS 3.1 1.3 - - - -
362B ARG* 3.0 27.2 + - - +
363B ASP* 3.3 7.3 + - - -
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Residues in contact with LEU 360 (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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53B SER 3.2 13.7 + - - -
55B GLN* 3.6 38.4 - - + +
58B ILE* 3.7 30.1 - - + -
355B VAL* 4.8 3.6 - - + -
356B LEU 3.0 9.5 + - - +
357B ILE* 3.4 11.9 - - + +
359B GLN* 1.3 73.0 - - - +
361B HIS* 1.3 64.3 + - + +
363B ASP* 2.9 27.0 + - - +
366B ILE* 5.7 0.2 - - - +
367B TRP* 3.9 4.9 + - - -
388B HIS 3.7 19.7 - - - +
389B ALA 3.5 18.4 - - - +
391B LYS* 3.9 24.5 - - + -
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Residues in contact with HIS 361 (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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322B LEU 3.3 16.2 + - - -
323B ARG* 2.8 68.5 + - + +
326B PRO* 3.9 2.9 - - + +
357B ILE* 3.0 36.1 + - + +
358B PRO 3.9 3.6 - - - +
359B GLN 3.1 0.6 - - - -
360B LEU* 1.3 78.2 - - + +
362B ARG* 1.4 54.4 + - - +
363B ASP 3.5 0.4 - - - -
367B TRP* 3.6 17.8 + + - +
389B ALA 3.4 19.5 - - - -
390B PHE* 3.5 20.0 - + - -
391B LYS 3.0 22.8 + - - -
392B PRO* 3.9 10.1 - - + -
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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