Contacts of the helix formed by residues 309 - 315 (chain G) in PDB entry 5DK3
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 LEU 309 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253G ILE* 5.6 4.0 - - + -
308G VAL* 1.4 75.5 - - - +
310G HIS* 1.3 85.3 + - + +
311G GLN* 3.3 21.3 - - + +
312G ASP* 3.2 36.8 + - - +
313G TRP* 3.3 12.0 + - - +
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Residues in contact with HIS 310 (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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249G ASP 3.1 20.4 + - - -
250G THR* 3.4 21.4 - - - +
251G LEU 4.9 0.2 - - - -
252G MET 2.8 19.9 + - - -
253G ILE* 3.7 36.7 - - + +
255G ARG 2.8 28.2 + - - -
256G THR* 4.8 1.3 - - - -
257G PRO* 3.7 18.1 - - + +
308G VAL 3.8 0.6 + - - -
309G LEU* 1.3 84.0 - - + +
311G GLN* 1.3 61.9 + - - +
313G TRP* 3.4 4.6 + - - +
314G LEU* 3.1 32.2 + - + +
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Residues in contact with GLN 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309G LEU* 3.3 17.6 - - + +
310G HIS* 1.3 78.1 - - - +
312G ASP* 1.4 57.3 + - - +
314G LEU* 4.5 6.7 - - - -
315G ASN* 2.8 49.6 + - - +
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Residues in contact with ASP 312 (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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279G VAL* 5.2 3.3 - - - +
309G LEU* 3.2 33.8 + - - +
311G GLN* 1.4 77.3 - - - +
313G TRP* 1.3 61.1 + - - +
315G ASN* 3.5 6.2 + - - +
316G GLY 3.0 15.6 - - - +
317G LYS* 3.2 47.1 + - + +
319G TYR* 3.1 22.5 + - - +
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Residues in contact with TRP 313 (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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244G PRO* 3.8 17.0 - - + -
245G PRO* 3.5 32.9 + - + +
250G THR* 3.5 33.5 + - + +
259G VAL* 4.0 10.5 - - + -
308G VAL* 4.3 11.0 - - + -
309G LEU 3.3 9.4 + - - +
310G HIS* 3.9 7.9 - - - +
312G ASP* 1.3 78.2 - - - +
314G LEU* 1.3 59.9 + - + +
316G GLY 3.0 24.4 + - - +
319G TYR* 3.6 38.0 + + - +
336G ILE* 4.3 5.6 - - + -
337G SER* 3.5 26.9 - - - -
338G LYS* 3.5 46.9 - - + +
376G ASP* 5.5 4.0 + - - -
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Residues in contact with LEU 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250G THR* 3.8 23.8 - - - +
251G LEU* 4.3 9.4 - - + -
310G HIS* 3.1 23.6 + - + +
311G GLN* 3.9 6.3 - - - +
313G TRP* 1.3 78.8 - - + +
315G ASN* 1.4 60.8 + - - +
316G GLY 3.2 1.8 + - - -
338G LYS* 3.0 29.5 + - + -
430G GLU* 4.0 34.6 - - + +
435G HIS* 3.6 31.4 - - + +
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Residues in contact with ASN 315 (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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311G GLN* 2.8 41.2 + - - +
312G ASP* 3.5 6.3 + - - +
313G TRP 3.4 0.4 - - - -
314G LEU* 1.4 76.7 + - - +
316G GLY* 1.3 58.5 + - - +
317G LYS* 3.7 10.3 + - + +
338G LYS* 5.3 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