Contacts of the helix formed by residues 305 - 311 (chain L) in PDB entry 3EXG
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 305 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111I GLY* 3.9 13.2 - - - +
119I GLY 3.1 16.1 + - - +
329I GLU* 4.1 4.3 - - - +
330I PRO* 3.6 34.3 - - + -
303L PRO* 4.6 0.4 - - - +
304L TYR* 1.3 83.1 - - - +
306L LYS* 1.3 67.5 + - - +
307L ILE* 4.6 0.2 - - + -
308L LEU* 3.0 13.9 + - + +
309L GLU* 2.8 20.8 + - - +
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Residues in contact with LYS 306 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I ARG* 3.8 46.7 - - - +
329I GLU* 3.5 17.2 + - - +
304L TYR 3.2 3.4 + - - -
305L ALA* 1.3 68.9 - - - +
307L ILE* 1.3 58.3 + - - +
309L GLU* 3.1 1.7 + - - +
310L ASP* 2.8 69.9 + - - +
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Residues in contact with ILE 307 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329I GLU* 3.4 30.4 + - + +
330I PRO* 3.6 26.9 - - + +
332I LEU* 4.7 16.8 - - + +
305L ALA* 4.6 0.4 - - + -
306L LYS* 1.3 80.4 - - - +
308L LEU* 1.3 78.9 + - + +
310L ASP* 3.3 4.3 + - + -
311L ASN* 3.1 40.0 + - - +
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Residues in contact with LEU 308 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119I GLY 5.5 0.2 - - - +
120I LYS* 3.6 33.2 - - + -
330I PRO* 3.9 25.4 - - + +
331I PRO 4.2 1.8 - - - +
332I LEU* 3.9 38.4 - - + +
334I GLU 4.5 1.8 - - - +
335I LEU* 3.5 26.6 - - + +
303L PRO* 3.6 20.4 - - + -
305L ALA* 3.0 8.5 + - + +
307L ILE* 1.3 94.1 - - + +
309L GLU* 1.3 62.9 + - - +
311L ASN 3.3 6.8 + - - -
312L SER* 3.2 18.5 + - - -
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Residues in contact with GLU 309 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I ARG* 2.7 30.9 + - - +
120L ALA* 6.0 1.0 - - - +
121L SER 4.2 6.6 + - - +
122L ALA* 3.6 9.1 + - - +
123L GLY* 2.8 29.9 + - - -
124L VAL 4.2 1.4 + - - -
125L ALA 4.7 0.3 + - - -
129L SER* 4.9 2.3 + - - -
302L MET* 4.0 20.6 - - - +
303L PRO* 3.8 23.1 - - - +
305L ALA 2.8 16.1 + - - +
306L LYS 3.5 3.4 - - - +
308L LEU* 1.3 77.0 - - - +
310L ASP* 1.3 63.0 + - - +
312L SER* 2.9 24.4 + - - -
313L ILE* 3.8 18.0 + - + +
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Residues in contact with ASP 310 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I ARG* 5.6 0.2 + - - -
306L LYS* 2.8 59.7 + - - +
307L ILE* 3.9 6.4 - - - +
309L GLU* 1.3 78.9 - - - +
311L ASN* 1.3 64.9 + - - +
312L SER 3.2 1.0 + - - -
313L ILE* 3.8 10.8 + - - +
315L GLN* 3.0 42.7 + - - +
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Residues in contact with ASN 311 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332I LEU* 3.3 39.3 - - + +
335I LEU* 3.8 14.8 - - + +
351I ALA* 4.9 7.0 + - - +
357I PHE* 4.4 13.1 - - + -
298L ALA* 3.9 7.6 - - - +
307L ILE* 3.1 32.5 + - - +
308L LEU 3.3 0.9 + - - -
309L GLU 3.1 1.4 - - - -
310L ASP* 1.3 83.9 - - - +
312L SER* 1.3 60.2 + - - +
313L ILE 3.5 4.2 - - - +
315L GLN* 5.4 3.4 - - - +
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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