Contacts of the helix formed by residues 315 - 324 (chain G) in PDB entry 40ER
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 315 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169G HIS* 3.5 17.3 - - + +
170G LYS* 3.4 43.7 - - + +
173G LEU* 3.6 16.2 - - + -
292G LEU* 3.5 35.0 - - + +
297G VAL 4.1 5.2 - - - +
298G HIS* 3.0 41.2 + - + +
314G SER* 1.3 74.8 + - - +
316G SER* 1.3 57.0 + - - +
318G ILE* 3.1 7.1 + - - -
319G LEU* 2.8 40.6 + - + +
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Residues in contact with SER 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G ILE* 5.3 3.5 - - - +
151G HIS* 5.1 1.9 + - - -
169G HIS* 3.7 27.8 + - - -
298G HIS* 4.2 0.5 + - - -
314G SER* 3.6 0.4 + - - -
315G LEU* 1.3 77.8 - - - +
317G ASP* 1.3 56.4 + - - +
319G LEU* 4.0 1.2 - - - +
320G GLN* 2.8 41.0 + - - +
403G AMP 2.8 43.5 + - - -
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Residues in contact with ASP 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198G ILE* 3.8 19.9 - - + +
199G GLY* 3.4 24.0 + - - -
312G ILE 3.5 1.2 - - - +
313G VAL* 3.6 3.3 - - + -
314G SER 2.8 34.2 + - - +
316G SER* 1.3 73.6 - - - +
318G ILE* 1.3 57.9 + - + +
320G GLN* 3.8 4.3 - - - +
321G ALA* 2.9 32.7 + - - +
403G AMP 2.6 41.6 + - - -
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Residues in contact with ILE 318 (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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173G LEU* 4.6 14.4 - - + -
189G MET* 5.7 2.0 - - + -
198G ILE* 4.9 5.2 - - + -
285G LEU* 5.1 7.9 - - + -
288G ILE* 5.3 3.4 - - + -
289G ILE* 3.9 38.6 - - + -
292G LEU* 3.6 29.6 - - + -
313G VAL* 4.3 10.1 - - + +
314G SER 3.2 25.8 - - - +
315G LEU* 3.1 11.7 + - + +
317G ASP* 1.3 76.3 - - + +
319G LEU* 1.3 65.4 + - + +
321G ALA* 3.3 11.6 + - - +
322G LEU* 3.2 37.5 + - + +
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Residues in contact with LEU 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G MET* 6.0 0.3 - - - +
142G VAL* 4.3 17.1 - - + +
145G LEU* 4.3 3.1 - - + -
146G ILE* 4.4 7.9 - - + -
169G HIS* 3.4 40.8 - - + +
172G ILE* 4.0 31.9 - - + -
173G LEU* 4.4 20.2 - - + +
315G LEU* 2.8 39.2 + - + +
316G SER* 4.0 3.1 - - - +
318G ILE* 1.3 76.2 - - + +
320G GLN* 1.3 60.5 + - - +
322G LEU* 3.3 19.8 + - + +
323G VAL* 3.4 20.3 + - - +
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Residues in contact with GLN 320 (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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146G ILE* 3.6 45.3 - - + +
316G SER* 2.8 27.8 + - - +
317G ASP* 4.0 5.5 - - - +
319G LEU* 1.3 72.2 - - - +
321G ALA* 1.3 58.3 + - - +
322G LEU 3.2 3.1 - - - -
323G VAL* 3.4 15.1 - - + +
324G LEU* 3.5 22.5 - - + +
403G AMP 5.6 1.9 + - - -
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Residues in contact with ALA 321 (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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26G ASN* 5.5 0.7 + - - -
188G PHE* 4.8 11.8 - - + -
198G ILE* 4.0 31.2 - - + -
317G ASP 2.9 18.2 + - - +
318G ILE* 3.7 6.7 - - - +
319G LEU 3.2 0.2 - - - -
320G GLN* 1.3 76.6 - - - +
322G LEU* 1.3 63.8 + - + +
324G LEU* 4.5 14.5 - - - +
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Residues in contact with LEU 322 (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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26G ASN* 3.7 9.0 + - - -
29G TYR* 4.0 36.4 - - + +
30G THR* 3.3 17.8 + - - -
33G MET* 4.6 17.9 - - + -
173G LEU* 6.1 2.9 - - + -
176G LEU* 5.3 12.8 - - + -
188G PHE* 4.1 22.9 - - + -
189G MET* 4.9 8.7 - - + -
285G LEU* 6.2 0.4 - - + -
318G ILE* 3.2 34.1 - - + +
319G LEU* 3.6 13.7 - - + +
320G GLN 3.2 0.2 - - - -
321G ALA* 1.3 80.3 - - + +
323G VAL* 1.3 66.7 + - - +
324G LEU 3.0 3.2 + - - -
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Residues in contact with VAL 323 (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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26G ASN* 4.7 1.4 + - - -
30G THR* 4.0 15.5 + - - +
33G MET* 4.4 14.1 - - + +
139G PHE* 4.1 19.0 - - + -
142G VAL* 3.5 35.2 - - + -
143G SER* 5.1 2.5 - - - +
146G ILE* 4.0 20.6 - - + -
319G LEU 3.5 11.4 - - - +
320G GLN* 3.4 17.5 - - + +
322G LEU* 1.3 75.6 - - - +
324G LEU* 1.3 69.9 + - + +
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Residues in contact with LEU 324 (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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26G ASN* 2.8 35.7 + - - +
320G GLN* 3.5 30.1 - - + +
321G ALA* 4.5 10.3 - - - -
322G LEU 3.1 4.2 - - - -
323G VAL* 1.3 87.0 - - + +
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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