Contacts of the helix formed by residues 354 - 362 (chain C) in PDB entry 1D1T
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 LYS 354 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350C LEU* 4.1 20.2 - - + +
351C PRO* 2.8 37.0 + - + +
353C LYS* 1.3 73.9 - - + +
355C ILE* 1.3 54.5 + - - +
356C SER* 3.1 4.7 - - - -
357C GLU* 2.7 69.3 + - - +
358C GLY 3.0 8.7 + - - -
372C LEU* 4.5 2.7 - - - -
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Residues in contact with ILE 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ALA* 3.6 24.7 - - + -
21C PHE* 3.8 32.3 - - + -
23C ILE* 4.2 18.4 - - + -
45C ILE* 4.9 0.2 - - - -
146C PHE* 3.8 15.5 - - + -
351C PRO 4.2 0.2 + - - -
352C PHE* 2.8 26.9 + - + +
353C LYS 3.8 7.4 - - - +
354C LYS* 1.3 76.0 - - - +
356C SER* 1.3 67.7 + - - +
358C GLY* 2.9 11.4 + - - -
359C PHE* 3.1 35.6 + - + -
372C LEU* 3.7 19.9 - - + +
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Residues in contact with SER 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PRO* 5.8 4.0 - - - +
21C PHE* 5.6 10.1 + - - -
353C LYS 4.3 3.1 + - - -
354C LYS* 3.1 3.3 - - - -
355C ILE* 1.3 85.4 - - - +
357C GLU* 1.3 61.2 + - - +
359C PHE* 3.4 8.3 + - - +
360C GLU* 3.3 24.6 + - - +
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Residues in contact with GLU 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C HIS* 5.8 0.2 - - - -
350C LEU* 3.0 30.5 - - - +
354C LYS* 2.7 52.8 + - - +
356C SER* 1.3 74.1 - - - +
358C GLY* 1.3 57.4 + - - +
360C GLU* 2.8 27.4 + - + +
361C LEU* 2.9 33.7 + - + +
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Residues in contact with GLY 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ILE* 3.7 23.0 - - - +
350C LEU* 4.7 2.1 - - - +
354C LYS 3.0 7.0 + - - -
355C ILE 2.9 8.9 + - - -
357C GLU* 1.3 76.7 - - - +
359C PHE* 1.3 56.3 + - - +
360C GLU 3.1 0.3 + - - -
361C LEU* 3.2 15.5 + - - +
362C LEU* 3.0 28.8 + - - +
370C THR* 4.4 10.6 + - - -
372C LEU* 5.6 0.4 - - - -
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Residues in contact with PHE 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C PHE* 3.8 14.4 - + + -
45C ILE* 3.5 34.3 - - + -
49C ASP* 4.1 15.3 - - + -
50C ASP* 3.3 27.4 - - + +
53C ILE* 3.5 23.8 - - + -
146C PHE* 3.5 24.5 - + - -
355C ILE* 3.1 40.3 + - + +
356C SER* 3.8 8.3 - - - +
357C GLU 3.3 0.4 - - - -
358C GLY* 1.3 74.3 - - - +
360C GLU* 1.3 58.8 + - - +
362C LEU* 4.6 4.9 - - + -
363C ASN* 2.9 32.4 + - - +
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Residues in contact with GLU 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C SER* 3.3 14.8 + - - +
357C GLU* 2.8 19.7 + - + +
359C PHE* 1.3 78.4 - - - +
361C LEU* 1.3 64.9 + - + +
363C ASN* 3.7 4.0 + - - +
364C SER* 3.2 22.3 + - - -
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Residues in contact with LEU 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C HIS* 3.8 44.2 - - + +
350C LEU* 4.3 14.1 - - + -
357C GLU* 2.9 33.0 + - + +
358C GLY* 3.5 13.9 - - - +
360C GLU* 1.3 76.9 - - + +
362C LEU* 1.3 67.1 + - - +
364C SER* 2.7 22.1 + - - -
365C GLY 3.2 5.7 + - - -
366C GLN* 3.3 25.9 + - + +
367C SER* 3.2 13.9 - - - +
370C THR* 4.6 3.1 - - - +
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Residues in contact with LEU 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ILE* 4.0 31.0 - - + +
46C CYS 4.3 0.9 - - - +
47C ARG* 3.4 54.8 + - - +
50C ASP* 4.6 12.6 - - + -
358C GLY 3.0 12.9 + - - +
359C PHE* 4.6 4.7 - - + -
361C LEU* 1.3 77.1 - - - +
363C ASN* 1.3 59.1 + - - +
364C SER 2.9 6.9 + - - -
365C GLY* 3.0 14.6 + - - -
367C SER* 3.1 15.8 + - - +
368C ILE 3.7 23.3 - - - +
369C ARG* 4.9 2.7 - - - +
370C THR* 5.5 3.4 - - - +
3377C NAD 4.6 13.2 - - - +
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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