Contacts of the helix formed by residues 328 - 340 (chain C) in PDB entry 1Y9A
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 GLU 328 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C TRP* 3.5 28.6 + - + +
326C GLY* 3.1 2.3 + - - +
327C LEU* 1.3 76.7 - - - +
329C LYS* 1.3 72.8 + - + +
330C VAL 3.2 1.7 + - - -
331C GLU* 3.2 17.3 + - - +
332C ASP* 3.7 3.6 - - - +
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Residues in contact with LYS 329 (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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324C PHE* 3.6 37.6 - - + -
325C GLU 3.5 21.4 + - - +
326C GLY* 3.0 12.0 + - - +
328C GLU* 1.3 84.7 - - + +
330C VAL* 1.3 59.0 + - - +
331C GLU 3.1 2.2 - - - -
332C ASP* 3.2 31.1 + - - +
333C ALA* 2.9 28.4 + - - +
349C VAL* 3.9 4.2 - - + +
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Residues in contact with VAL 330 (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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4C LEU* 4.0 12.6 - - + +
14C TRP* 3.7 18.4 - - + -
34C LEU* 3.7 30.5 - - + -
36C PRO* 6.6 0.2 - - + -
120C PHE* 4.0 35.6 - - + -
327C LEU* 3.2 20.1 + - + +
329C LYS* 1.3 77.2 - - - +
331C GLU* 1.3 58.8 + - - +
333C ALA* 3.8 3.0 - - + +
334C LEU* 2.9 30.7 + - - +
349C VAL* 4.0 22.8 - - + +
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Residues in contact with GLU 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 3.8 13.9 - - + -
12C ILE* 4.3 21.5 - - + +
13C GLY* 6.3 0.2 - - - -
14C TRP* 2.8 38.5 + - - +
328C GLU 3.2 13.3 + - - +
329C LYS 3.1 0.4 - - - -
330C VAL* 1.3 78.1 - - - +
332C ASP* 1.3 67.7 + - - +
334C LEU* 3.2 3.7 + - - +
335C MET* 3.0 34.6 + - + +
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Residues in contact with ASP 332 (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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324C PHE* 4.3 13.4 - - + -
328C GLU 3.7 4.7 - - - +
329C LYS* 3.2 45.6 + - + +
331C GLU* 1.3 79.6 - - - +
333C ALA* 1.3 63.0 + - - +
335C MET* 3.4 8.0 + - - +
336C LEU* 3.2 26.1 + - - +
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Residues in contact with ALA 333 (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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36C PRO* 3.5 29.4 - - + +
324C PHE* 4.2 4.5 - - + -
329C LYS 2.9 15.9 + - - +
330C VAL* 3.8 5.2 - - - +
332C ASP* 1.3 78.4 - - - +
334C LEU* 1.3 62.3 + - - +
336C LEU* 3.2 27.6 + - - +
337C MET* 3.4 5.0 + - - +
347C PRO* 3.8 11.5 - - + +
349C VAL* 4.0 19.7 - - + -
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Residues in contact with LEU 334 (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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4C LEU* 4.5 5.4 - - + -
12C ILE* 4.2 18.4 - - + -
36C PRO* 3.8 17.6 - - + +
37C CYS 4.0 12.1 - - - +
40C ASP* 3.9 26.5 - - + +
41C THR* 4.2 10.3 - - + +
44C VAL* 5.5 0.2 - - + -
45C TRP* 4.4 15.0 - - + -
57C LEU* 3.8 28.9 - - + -
120C PHE* 4.9 8.5 - - + -
330C VAL 2.9 18.2 + - - +
331C GLU* 3.8 4.5 - - - +
333C ALA* 1.3 76.0 - - - +
335C MET* 1.3 63.5 + - - +
337C MET* 3.1 6.9 + - + +
338C LYS* 3.0 19.6 + - - +
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Residues in contact with MET 335 (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 ILE* 4.3 13.0 - - - -
45C TRP* 4.0 24.2 - - + -
331C GLU* 3.0 28.8 + - + +
332C ASP* 3.7 8.7 - - - +
333C ALA 3.3 0.2 - - - -
334C LEU* 1.3 73.2 - - - +
336C LEU* 1.3 64.5 + - - +
338C LYS* 3.2 29.2 + - + +
339C ASN* 2.9 46.4 + - - +
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Residues in contact with LEU 336 (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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322C HIS* 4.1 22.4 - - + +
324C PHE* 3.9 32.5 - - + -
332C ASP 3.2 12.5 + - - +
333C ALA* 3.2 8.1 + - - +
335C MET* 1.3 75.7 - - - +
337C MET* 1.3 55.3 + - - +
339C ASN* 5.0 1.6 - - + -
340C LYS* 2.7 34.3 + - - -
341C PRO* 3.5 24.8 - - + +
344C LEU* 3.4 17.2 - - + +
347C PRO* 4.0 16.2 - - + -
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Residues in contact with MET 337 (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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36C PRO* 3.6 34.5 - - + +
37C CYS 4.3 1.6 - - - +
38C THR* 3.7 35.9 + - - +
41C THR* 3.9 18.4 + - + +
177C PRO* 5.3 4.3 - - + -
333C ALA 3.5 12.1 - - - +
334C LEU* 3.1 6.7 + - + +
336C LEU* 1.3 76.8 - - - +
338C LYS* 1.3 61.5 + - - +
340C LYS* 3.2 17.9 - - - +
344C LEU* 4.0 14.1 - - + -
345C ILE 4.0 14.1 - - - +
346C LYS* 4.0 11.9 - - + +
347C PRO* 3.5 25.1 - - - -
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Residues in contact with LYS 338 (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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41C THR* 3.8 14.8 - - + +
45C TRP* 3.3 56.2 - - + +
334C LEU 3.0 11.5 + - - +
335C MET* 3.2 34.7 + - + +
337C MET* 1.3 78.9 - - - +
339C ASN* 1.3 67.7 + - - +
340C LYS* 3.5 18.9 + - - +
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Residues in contact with ASN 339 (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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335C MET* 2.9 39.1 + - - +
336C LEU* 4.4 1.8 - - + +
338C LYS* 1.3 92.9 + - - +
340C LYS* 1.3 77.2 + - - +
341C PRO* 3.6 6.5 - - + +
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Residues in contact with LYS 340 (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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38C THR* 6.1 3.6 - - + +
200C ARG* 5.4 4.1 + - - +
336C LEU 2.7 18.9 + - - -
337C MET* 3.2 21.3 - - - +
338C LYS 3.5 14.7 + - - +
339C ASN* 1.3 78.9 + - - +
341C PRO* 1.3 69.5 - - - +
344C LEU* 4.3 6.3 - - + -
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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