Contacts of the helix formed by residues 357 - 364 (chain C) in PDB entry 1YA8
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 TRP 357 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C LEU* 4.4 11.9 - - + -
355C PHE 3.4 2.6 + - - -
356C GLY* 1.3 82.2 - - - +
358C LEU* 1.3 98.0 + - + +
359C ILE 3.2 2.0 - - - -
360C PRO* 3.0 7.8 - - - +
361C MET* 2.7 59.6 + - + +
457C SER* 3.5 31.6 - - - -
459C MET* 2.9 41.1 + - + -
460C LYS* 3.7 22.0 - - + -
461C PRO* 3.6 18.8 - - + +
464C VAL* 4.3 7.9 - - + -
467C ASP* 2.9 20.5 + - - +
2031C MVB 4.2 24.8 + - + +
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Residues in contact with LEU 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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97C LEU* 5.0 1.3 - - + -
100C LEU* 3.5 33.9 - - + -
101C PHE* 3.3 40.4 - - + -
357C TRP* 1.3 93.5 - - + +
359C ILE* 1.3 60.7 + - + +
361C MET* 3.6 2.5 - - - +
363C LEU* 3.0 53.8 + - + +
467C ASP* 3.0 19.8 + - - +
468C HIS* 3.4 24.9 - - + +
4003C SMB 6.3 1.3 - - + -
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Residues in contact with ILE 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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354C GLU 3.6 11.6 + - - +
355C PHE* 3.2 24.9 - - + -
357C TRP 4.7 0.2 - - - +
358C LEU* 1.3 75.6 - - + +
360C PRO* 1.3 73.1 - - + +
361C MET 3.0 2.5 + - - -
363C LEU* 3.5 5.1 + - - +
364C MET* 3.3 39.1 + - + +
388C LEU* 5.9 0.9 - - + -
425C MET* 4.8 4.0 - - + -
426C PHE* 3.9 22.4 - - + -
468C HIS* 3.6 43.4 - - + +
4003C SMB 4.5 24.7 - - + -
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Residues in contact with PRO 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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355C PHE* 3.2 53.4 - - + +
356C GLY 4.8 0.7 - - - -
357C TRP 3.0 22.7 - - - +
359C ILE* 1.3 89.4 - - + +
361C MET* 1.3 58.0 + - - +
364C MET* 3.9 0.6 - - + -
365C SER 3.3 1.4 + - - -
366C TYR* 2.8 51.5 + - + +
368C LEU* 5.3 0.7 - - + -
418C LEU* 4.5 4.3 - - + -
2031C MVB 4.5 18.7 + - + +
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Residues in contact with MET 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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96C LEU* 4.7 15.0 - - + -
100C LEU* 4.8 7.2 - - + -
357C TRP* 2.7 52.3 + - + +
358C LEU* 3.6 4.9 - - - +
360C PRO* 1.3 74.0 - - - +
363C LEU* 1.3 91.4 + - + +
364C MET 2.9 3.8 - - - -
365C SER* 2.7 28.3 + - - +
459C MET* 3.9 27.6 - - + -
2031C MVB 4.5 7.6 + - - +
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Residues in contact with LEU 363 (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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96C LEU* 3.9 23.3 - - + -
97C LEU* 4.0 20.2 - - + +
100C LEU* 3.9 14.4 - - + -
304C LEU* 3.8 30.5 - - + +
305C SER* 5.3 0.7 - - - -
358C LEU* 3.0 44.8 + - + +
359C ILE* 3.5 4.5 + - - +
361C MET* 1.3 95.2 - - - +
364C MET* 1.3 59.6 + - + +
365C SER* 3.5 3.1 + - - -
4003C SMB 4.4 20.4 - - + -
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Residues in contact with MET 364 (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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303C PHE 6.0 0.4 - - - +
304C LEU* 2.9 31.6 - - + +
305C SER* 4.0 5.3 + - - +
306C LEU* 3.5 47.4 + - + +
355C PHE* 5.4 2.2 - - - -
359C ILE* 3.3 32.1 + - + +
360C PRO* 4.4 3.4 - - + +
361C MET 2.8 1.6 + - - -
363C LEU* 1.3 78.3 - - + +
365C SER* 1.3 74.0 + - - +
366C TYR* 3.4 6.3 + - + +
388C LEU* 3.4 40.8 - - + -
4003C SMB 5.2 11.2 - - + -
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Residues in contact with SER 365 (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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305C SER* 4.8 8.4 + - - -
306C LEU 5.6 1.2 - - - +
308C LEU* 5.8 2.3 - - - +
360C PRO 3.8 0.2 - - - -
361C MET 2.7 16.5 + - - -
363C LEU 4.6 2.6 + - - -
364C MET* 1.3 82.1 - - - +
366C TYR* 1.3 67.2 + - - +
367C PRO* 3.3 5.5 - - - +
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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