Contacts of the helix formed by residues 315 - 325 (chain I) in PDB entry 5G04
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 ALA 315 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314I SER* 1.3 74.5 - - - +
316I GLU* 1.3 66.3 + - - +
317I LEU 3.3 0.7 - - - -
318I GLN* 3.1 17.1 + - - +
319I THR* 3.4 15.8 + - - +
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Residues in contact with GLU 316 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290I PHE* 4.6 7.5 - - + -
294I LYS* 3.4 30.3 - - + +
295I ASN* 3.5 28.4 + - - +
303I GLU* 3.6 22.7 - - - +
314I SER* 3.7 5.6 + - - +
315I ALA* 1.3 78.5 - - - +
317I LEU* 1.3 61.5 + - - +
319I THR* 3.2 8.9 + - - +
320I LEU* 3.2 23.3 + - - +
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Residues in contact with LEU 317 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290I PHE* 3.8 8.3 - - + -
303I GLU* 3.4 58.6 - - + +
304I PHE* 4.1 18.2 - - + +
307I LEU* 4.3 19.3 - - + -
313I ALA* 3.4 23.1 - - + +
314I SER* 4.1 5.3 + - - +
315I ALA 3.3 0.4 - - - -
316I GLU* 1.3 75.8 - - - +
318I GLN* 1.3 58.1 + - - +
320I LEU* 3.6 25.2 - - + +
321I LEU* 2.7 44.2 + - + +
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Residues in contact with GLN 318 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312I LYS 4.2 7.3 - - - +
313I ALA* 5.2 4.1 - - + +
314I SER 4.0 15.8 + - - +
315I ALA* 3.1 13.3 + - - +
317I LEU* 1.3 78.1 - - - +
319I THR* 1.3 61.8 + - + +
321I LEU* 4.9 0.9 - - - -
322I MET* 3.5 47.0 + - + +
428I MET* 4.0 42.1 + - - +
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Residues in contact with THR 319 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315I ALA 3.4 8.5 + - - +
316I GLU* 3.2 13.7 + - - +
318I GLN* 1.3 75.5 - - + +
320I LEU* 1.3 66.1 + - - +
323I ASN* 2.9 42.3 + - - +
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Residues in contact with LEU 320 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286I ARG 5.6 1.8 - - - +
289I LYS* 5.9 0.7 - - + -
290I PHE* 3.5 57.7 - - + -
304I PHE* 6.0 3.8 - - + -
316I GLU* 3.2 15.5 + - + +
317I LEU* 3.6 18.4 - - + +
319I THR* 1.3 82.6 + - - +
321I LEU* 1.3 66.4 + - + +
324I GLN* 3.3 55.3 + - - +
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Residues in contact with LEU 321 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304I PHE* 5.1 12.6 - - + -
307I LEU* 4.7 16.6 - - + -
317I LEU* 2.7 24.5 + - + +
318I GLN* 4.5 2.5 - - - +
320I LEU* 1.3 78.3 - - + +
322I MET* 1.3 64.0 + - + +
325I LEU* 2.6 54.6 + - + +
421I LEU* 3.9 31.2 - - + -
424I ALA* 6.4 0.7 - - + -
425I MET* 3.8 30.5 - - + -
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Residues in contact with MET 322 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318I GLN* 3.5 46.5 + - + +
321I LEU* 1.3 93.1 - - + +
323I ASN* 1.3 68.9 + - - +
325I LEU 3.0 19.7 - - - +
326I THR* 3.6 15.1 - - - +
425I MET* 5.0 15.3 - - + +
428I MET* 3.7 36.3 - - + +
429I THR* 6.3 3.8 - - + -
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Residues in contact with ASN 323 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319I THR* 2.9 34.4 + - - +
321I LEU 3.5 0.4 - - - -
322I MET* 1.3 82.3 - - - +
324I GLN* 1.3 66.8 + - + +
326I THR* 5.3 3.1 - - - +
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Residues in contact with GLN 324 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286I ARG* 2.8 58.4 + - - +
289I LYS* 2.8 36.8 + - - +
320I LEU* 3.3 43.6 + - - +
321I LEU 4.4 0.2 - - - +
323I ASN* 1.3 80.8 - - + +
325I LEU* 1.3 56.7 + - + +
326I THR* 4.4 0.4 - - - -
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Residues in contact with LEU 325 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283I MET* 6.2 2.0 - - - -
286I ARG* 4.1 29.2 - - + +
321I LEU* 2.6 43.4 + - + +
322I MET* 3.0 14.9 - - - +
323I ASN 3.4 0.4 - - - -
324I GLN* 1.3 79.5 - - + +
326I THR* 1.3 81.5 + - - +
329I GLY* 4.2 2.5 - - - -
330I LEU* 3.7 36.3 - - + +
333I LEU* 3.8 22.2 - - + -
421I LEU* 5.7 2.5 - - + -
425I MET* 4.2 11.4 - - + +
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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