Contacts of the helix formed by residues 301 - 312 (chain C) in PDB entry 1YO5
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 ASN 301 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C ALA* 3.3 13.7 - - - -
299C ALA 3.5 3.7 + - - +
300C MET* 1.3 80.0 - - - +
302C TYR* 1.3 58.9 + - - +
303C ASP* 3.4 16.5 + - - +
304C LYS* 3.0 40.3 + - - +
305C LEU* 2.9 25.5 + - - +
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Residues in contact with TYR 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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3A G 3.9 28.5 - - + +
4A C 2.8 29.3 + - - -
281C ILE* 3.6 24.5 - - + -
284C SER* 3.6 40.2 - - - +
285C ALA* 4.8 1.9 - - - +
287C VAL* 5.7 1.1 - - + -
288C ALA* 3.4 8.1 - - + +
301C ASN* 1.3 73.8 - - - +
303C ASP* 1.3 61.8 + - - +
305C LEU* 4.2 14.4 - - + -
306C SER* 2.8 54.0 + - - -
327C LEU* 3.4 23.2 - - + +
329C TYR* 3.0 21.5 + + - -
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Residues in contact with ASP 303 (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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2A A 6.1 0.3 - - - +
3A G 5.0 19.1 + - - +
4A C 5.3 7.8 + - - -
301C ASN* 3.4 16.1 + - - +
302C TYR* 1.3 77.8 - - - +
304C LYS* 1.3 60.7 + - + +
306C SER* 2.9 18.1 + - - -
307C ARG* 3.1 15.8 + - - +
310C ARG* 4.5 4.3 + - - -
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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
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5B A 4.6 2.0 + - + -
6B T 2.8 85.0 + - + +
7B C 5.0 9.6 + - + +
299C ALA* 2.9 32.1 + - - +
300C MET* 3.9 14.1 - - + +
301C ASN* 3.0 31.5 + - - +
303C ASP* 1.3 78.6 - - + +
305C LEU* 1.3 67.0 + - - +
307C ARG* 3.4 3.9 + - - +
308C SER* 3.4 18.7 + - - -
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Residues in contact with LEU 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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5B A 5.2 0.4 - - - -
251C LEU* 3.6 17.3 - - + +
255C LEU* 5.0 1.8 - - + -
281C ILE* 4.9 2.2 - - + -
287C VAL* 3.9 19.3 - - + +
288C ALA* 3.8 16.8 - - + +
291C TRP* 3.6 40.2 - - + +
300C MET* 3.6 10.6 - - - -
301C ASN 2.9 17.8 + - - +
302C TYR* 3.3 19.3 + - + +
304C LYS* 1.3 75.2 - - - +
306C SER* 1.3 65.8 + - - +
308C SER* 3.1 18.2 + - - -
309C ILE* 3.2 32.3 + - + -
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Residues in contact with SER 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A G 5.8 0.5 - - - +
4A C 4.3 3.8 + - - -
302C TYR* 2.8 55.8 + - - -
303C ASP* 2.9 15.9 + - - -
305C LEU* 1.3 73.4 - - - +
307C ARG* 1.3 64.4 + - - +
309C ILE* 3.1 11.0 + - - +
310C ARG* 3.0 41.4 + - - +
329C TYR* 3.9 10.0 + - - -
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Residues in contact with ARG 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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6A G 3.2 52.3 + - - +
7A G 2.7 43.2 + - - -
8A A 4.3 1.8 - - - +
5B A 5.7 0.4 - - - +
6B T 3.5 29.7 + - + +
7B C 4.0 4.5 - - - +
8B C 6.0 0.4 - - - +
303C ASP 3.1 15.1 + - - +
304C LYS* 3.6 10.5 - - - +
305C LEU 3.3 0.4 - - - -
306C SER* 1.3 77.3 + - - +
308C SER* 1.3 59.9 + - - +
310C ARG* 3.4 22.3 + - - +
311C GLN* 2.9 45.1 + - + +
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Residues in contact with SER 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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4B C 3.5 42.0 - - - +
5B A 3.8 14.1 + - - -
6B T 5.1 0.2 - - - +
251C LEU* 3.8 15.7 - - - -
304C LYS 3.4 7.1 + - - -
305C LEU 3.1 12.3 + - - -
307C ARG* 1.3 75.7 - - - +
309C ILE* 1.3 65.1 + - - +
311C GLN* 3.3 23.1 + - - +
312C TYR* 3.6 12.5 + - - -
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Residues in contact with ILE 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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251C LEU* 3.7 17.9 - - + -
255C LEU* 4.2 18.2 - - + -
279C PHE* 5.3 0.9 - - + -
281C ILE* 4.3 7.4 - - + -
305C LEU* 3.2 25.7 + - + +
306C SER* 3.1 12.4 + - - +
308C SER* 1.3 75.0 - - - +
310C ARG* 1.3 57.7 + - - +
312C TYR* 2.8 35.1 + - + +
313C TYR* 3.8 6.0 + - + -
318C ILE* 3.7 22.2 - - + -
329C TYR* 3.7 51.4 - - + -
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Residues in contact with ARG 310 (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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4A C 3.8 23.2 + - - +
5A A 3.2 62.0 + - + +
6A G 3.0 45.3 + - + +
8B C 5.1 1.4 - - - +
303C ASP 4.5 4.4 + - - -
306C SER* 3.0 33.5 + - - +
307C ARG* 3.5 35.3 - - - +
308C SER 3.3 0.2 - - - -
309C ILE* 1.3 77.0 - - + +
311C GLN* 1.3 60.2 + - - +
312C TYR 3.0 0.2 - - - -
313C TYR* 3.0 39.5 + - + +
314C LYS 4.5 0.7 + - - -
329C TYR* 5.3 2.1 + - - +
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Residues in contact with GLN 311 (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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8A A 4.3 9.7 + - - -
9A T 5.5 0.2 - - - +
4B C 5.7 11.0 - - + -
5B A 4.7 8.2 + - - +
307C ARG* 2.9 46.3 + - + +
308C SER* 3.5 14.1 - - - +
309C ILE 3.2 0.6 - - - -
310C ARG* 1.3 76.0 - - - +
312C TYR* 1.3 62.2 + - + +
313C TYR 3.3 0.6 + - - -
314C LYS* 4.0 20.7 - - - +
315C LYS* 3.6 20.2 + - - +
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Residues in contact with TYR 312 (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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3B A 6.1 0.4 - - + -
4B C 2.6 33.5 + - - -
251C LEU* 3.3 20.9 + - + +
252C TRP* 3.1 49.8 + + + -
308C SER 3.7 12.3 - - - -
309C ILE* 2.8 20.9 + - - +
311C GLN* 1.3 80.0 - - + +
313C TYR* 1.3 61.2 + - - +
314C LYS 3.4 0.2 - - - -
315C LYS* 3.2 8.1 + - + +
316C GLY 3.1 18.7 + - - -
317C ILE* 3.2 30.4 + - + -
318C ILE* 3.5 35.8 - - + +
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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
------------------------------------------------------------
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