Contacts of the helix formed by residues 300 - 311 (chain C) in PDB entry 1YAA
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 ALA 300 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C HIS 5.4 0.4 - - - -
69C GLU 4.2 4.9 - - - +
71C LEU* 3.9 23.9 - - + +
298C PRO 3.4 0.2 + - - -
299C PRO* 1.3 70.8 - - - +
301C TYR* 1.3 69.4 + - - +
303C ALA* 3.2 5.7 + - - +
304C LYS* 3.2 40.0 + - - +
264D GLY* 2.7 26.9 + - - +
265D GLU* 3.6 13.7 + - - +
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Residues in contact with TYR 301 (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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57C GLU* 2.8 25.0 + - - +
60C ILE* 4.5 10.5 - - + -
61C HIS* 2.9 32.2 + + - -
66C TYR* 3.6 35.0 - + - -
265C GLU* 4.5 5.6 - - - +
299C PRO 3.8 0.2 - - - -
300C ALA* 1.3 76.5 - - - +
302C GLY* 1.3 65.9 + - - +
304C LYS* 3.1 20.3 + - + +
305C ILE* 3.3 30.2 + - + +
61D HIS* 3.4 2.3 + - - -
66D TYR* 3.7 8.5 - - - -
68D HIS* 4.7 1.8 - + - -
265D GLU* 3.1 24.3 + - - +
301D TYR* 3.3 45.3 - + + -
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Residues in contact with GLY 302 (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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262C MET* 4.2 4.4 - - - +
265C GLU* 3.9 22.8 + - - +
267C VAL* 3.3 27.6 - - - +
299C PRO* 4.6 4.0 + - - +
300C ALA 3.5 0.6 - - - -
301C TYR* 1.3 79.3 - - - +
303C ALA* 1.3 61.0 + - - +
305C ILE* 3.3 14.8 + - - +
306C VAL* 3.4 13.9 + - - +
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Residues in contact with ALA 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 4.7 1.6 - - + -
76C LEU* 3.9 11.4 - - + +
79C LEU* 3.7 22.1 - - + +
104C GLN* 3.3 38.8 - - - +
267C VAL* 3.8 7.6 - - + +
299C PRO 3.8 2.9 + - - +
300C ALA 3.2 9.9 + - - +
302C GLY* 1.3 75.8 - - - +
304C LYS* 1.3 58.1 + - - +
306C VAL 3.6 0.5 + - - -
307C ALA* 3.0 29.5 + - - +
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Residues in contact with LYS 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ILE* 3.3 31.9 - - + +
66C TYR* 4.9 5.4 - - + -
67C ASN* 2.9 39.7 + - - +
68C HIS* 4.8 0.8 - - - +
69C GLU 5.1 2.0 + - - +
71C LEU* 4.8 11.7 - - + -
76C LEU* 4.0 19.5 - - + -
300C ALA* 3.2 33.9 + - - +
301C TYR* 3.1 12.5 + - - +
303C ALA* 1.3 75.0 - - - +
305C ILE* 1.3 63.6 + - - +
307C ALA* 3.5 3.1 + - - +
308C LYS* 3.2 21.8 + - - +
265D GLU* 4.7 2.0 + - - -
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Residues in contact with ILE 305 (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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53C VAL* 4.2 24.5 - - + +
56C ALA* 3.6 20.0 - - + +
57C GLU* 3.4 27.1 - - + -
60C ILE* 3.3 21.3 - - + -
262C MET* 4.2 18.8 - - + -
265C GLU* 5.5 0.4 - - + -
301C TYR* 3.3 36.0 + - + +
302C GLY* 3.6 8.7 - - - +
303C ALA 3.3 0.2 - - - -
304C LYS* 1.3 74.9 - - - +
306C VAL* 1.3 67.1 + - + +
308C LYS 3.3 2.3 + - - -
309C LEU* 3.0 20.3 + - + +
68D HIS* 4.4 9.4 - - + +
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Residues in contact with VAL 306 (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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79C LEU* 4.1 18.2 - - + -
256C PHE* 3.9 33.2 - - + -
260C ALA* 4.7 5.2 - - + -
262C MET* 3.6 28.3 - - + -
267C VAL* 3.6 11.0 - - + -
302C GLY 3.4 16.7 + - - +
303C ALA 4.2 2.9 - - - +
305C ILE* 1.3 77.0 - - + +
307C ALA* 1.3 62.6 + - - +
309C LEU* 3.3 16.9 + - + +
310C LEU* 3.0 31.2 + - + +
319C TRP* 6.3 0.2 - - + -
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Residues in contact with ALA 307 (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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76C LEU* 3.9 10.3 - - + -
78C SER* 3.5 27.4 - - - +
79C LEU* 4.3 13.4 - - - +
82C ASN* 4.8 0.2 + - - -
303C ALA 3.0 20.3 + - - +
304C LYS* 3.6 5.8 - - - +
305C ILE 3.2 0.4 - - - -
306C VAL* 1.3 78.0 - - - +
308C LYS* 1.3 63.4 + - - +
310C LEU* 3.4 3.6 + - - +
311C GLU* 3.1 33.5 + - - +
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Residues in contact with LYS 308 (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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56C ALA* 4.2 14.8 - - + +
59C LEU* 4.4 17.0 - - + -
60C ILE* 3.9 17.5 - - + +
78C SER* 5.4 0.4 + - - -
304C LYS 3.2 16.6 + - - +
305C ILE 3.3 4.9 + - - +
307C ALA* 1.3 79.6 - - - +
309C LEU* 1.3 64.1 + - - +
311C GLU* 2.9 28.9 + - - -
312C THR* 3.1 45.0 + - - +
315C LEU* 3.7 6.4 - - + +
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Residues in contact with LEU 309 (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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52C SER* 3.5 44.2 - - - +
53C VAL* 4.0 21.1 - - + -
56C ALA* 4.4 1.5 - - + +
260C ALA* 4.3 13.2 - - + -
305C ILE 3.0 12.5 + - - +
306C VAL* 3.3 21.8 - - + +
307C ALA 3.2 0.2 - - - -
308C LYS* 1.3 80.7 - - - +
310C LEU* 1.3 51.0 - - + +
312C THR 3.5 0.7 - - - +
315C LEU* 3.5 19.7 - - + +
316C THR* 2.6 40.4 + - - -
319C TRP* 3.9 31.9 - - + -
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Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LEU* 4.8 3.8 - - + +
82C ASN* 3.9 47.9 - - + +
83C ALA* 4.1 9.9 - - + +
86C ILE* 4.0 16.8 - - + -
256C PHE* 4.5 6.5 - - + -
306C VAL* 3.0 35.7 + - + +
307C ALA* 4.1 2.5 - - - +
309C LEU* 1.3 76.4 - - + +
311C GLU* 1.3 60.5 + - - +
316C THR* 3.4 18.3 + - + +
319C TRP* 3.6 36.3 - - + -
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Residues in contact with GLU 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C SER* 3.7 28.9 + - - -
82C ASN* 3.2 22.6 + - - +
307C ALA 3.1 18.3 + - - +
308C LYS* 2.9 36.9 + - - +
310C LEU* 1.3 79.0 - - - +
312C THR* 1.3 60.2 + - - +
313C PRO* 3.2 14.2 - - - +
316C THR* 4.6 0.2 - - - -
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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