Contacts of the helix formed by residues 368 - 373 (chain G) in PDB entry 1YYL
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 ASP 368 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367G GLY* 1.3 75.3 - - - +
369G PRO* 1.3 69.9 - - - +
370G GLU* 3.2 14.6 - - - +
371G ILE* 2.9 18.2 + - + +
372G VAL* 2.9 8.0 + - - +
425G ASN* 3.2 24.3 + - - +
22M SER 5.0 0.7 - - - +
23M BIF 3.9 9.8 - - + +
24M CYS* 2.9 46.3 + - - +
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Residues in contact with PRO 369 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367G GLY 3.6 1.5 - - - +
368G ASP* 1.3 85.3 - - + +
370G GLU* 1.3 67.7 + - - +
372G VAL* 4.3 7.4 - - + -
373G THR* 2.8 43.1 + - + +
384G TYR* 3.8 8.7 - - + -
421G LYS* 3.4 30.7 - - - +
425G ASN* 3.8 8.5 - - - +
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Residues in contact with GLU 370 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257G THR* 2.9 17.2 + - - -
368G ASP* 3.3 3.8 - - - +
369G PRO* 1.3 81.6 - - - +
371G ILE* 1.3 53.8 + - - +
373G THR 2.8 22.2 - - - +
375G SER* 3.0 15.6 + - - +
384G TYR* 2.6 38.1 + - + +
421G LYS* 5.1 0.9 + - - -
424G ILE* 3.9 1.0 - - - +
425G ASN* 3.0 49.5 + - - -
23M BIF 3.5 43.1 - - + -
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Residues in contact with ILE 371 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257G THR* 4.8 3.7 - - + -
258G GLN* 3.4 17.8 + - - +
364G SER* 3.9 10.3 + - - +
366G GLY 3.8 12.3 - - - +
368G ASP* 2.9 11.9 + - + +
370G GLU* 1.3 77.1 - - - +
372G VAL* 1.3 65.1 + - - +
373G THR 3.3 1.7 + - - +
470G PRO 5.0 3.9 - - - +
471G GLY* 5.1 5.1 - - - +
472G GLY 3.5 25.4 - - - +
473G GLY* 3.8 3.6 - - - -
20M ALA* 3.9 8.1 - - + -
23M BIF 3.7 38.4 - - + -
24M CYS 3.6 18.8 - - - +
25M ALA* 3.7 20.9 - - + -
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Residues in contact with VAL 372 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258G GLN* 3.4 10.5 + - - -
364G SER* 3.9 17.7 + - - +
366G GLY* 3.5 12.8 - - - +
367G GLY 3.2 42.6 - - - +
368G ASP 2.9 7.4 + - - +
369G PRO* 3.8 7.6 - - + +
371G ILE* 1.3 75.6 - - - +
373G THR* 1.3 66.4 + - + +
387G SER* 4.1 4.9 + - - -
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Residues in contact with THR 373 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257G THR* 3.2 3.8 + - - -
258G GLN* 3.5 11.8 - - - +
369G PRO* 2.8 26.9 + - + +
370G GLU 2.8 20.4 - - - +
371G ILE 3.7 0.2 - - - +
372G VAL* 1.3 86.0 - - + +
374G HIS* 1.3 67.3 + - - +
375G SER* 3.1 3.5 + - - -
384G TYR* 3.8 25.1 - - + +
385G CYS 3.1 20.4 + - - +
386G ASN* 5.1 4.0 - - - -
387G SER* 4.4 2.2 - - - +
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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