Contacts of the helix formed by residues 303 - 308 (chain F) in PDB entry 3DV0
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 303 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299F PRO* 4.3 4.5 - - + -
300F PHE 2.6 18.6 + - - +
302F GLN* 1.3 71.8 - - - +
304F GLU* 1.3 61.7 + - - -
305F SER* 3.3 3.1 - - - -
306F VAL* 3.4 15.3 - - + +
307F TRP* 3.2 22.7 + - - +
338G GLN* 3.9 31.2 - - + +
343G LEU* 4.1 21.1 - - + -
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Residues in contact with GLU 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F GLY* 3.5 2.3 - - - -
121F GLY* 2.9 36.3 + - - -
123F HIS* 3.3 34.4 + - + +
124F THR 4.5 4.5 + - - +
129F SER* 4.5 1.0 + - - -
298F TYR* 2.8 27.7 + - + +
299F PRO* 4.3 13.0 - - + -
300F PHE 3.8 0.8 + - - -
301F ALA* 3.2 24.7 + - - +
302F GLN 3.4 0.8 - - - -
303F ALA* 1.3 77.2 - - - +
305F SER* 1.3 58.8 + - - +
308F LEU* 2.8 49.7 + - + +
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Residues in contact with SER 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F HIS* 6.0 2.4 - - - -
302F GLN 4.4 10.1 + - - -
303F ALA 4.7 0.2 - - - -
304F GLU* 1.3 80.4 - - - +
306F VAL* 1.3 69.0 + - - +
307F TRP 3.4 0.2 - - - -
308F LEU 4.5 6.8 - - - +
310F ASN* 4.7 9.7 + - - -
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Residues in contact with VAL 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F ALA* 3.4 22.0 - - + +
305F SER* 1.3 87.6 + - - +
307F TRP* 1.3 59.2 + - + +
308F LEU 5.0 0.9 - - - -
338G GLN 3.7 23.3 - - - +
339G LYS* 4.8 0.9 - - - -
340G VAL* 2.9 32.3 - - + +
343G LEU* 5.8 0.2 - - + -
362G TYR* 4.2 7.8 - - - -
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Residues in contact with TRP 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F GLU 4.2 4.7 - - - -
262F ALA* 5.5 0.7 - - - -
263F GLN* 3.8 27.6 - - + -
293F ALA* 3.3 20.3 - - + -
294F PRO* 3.6 54.8 + - + +
296F THR* 2.8 24.1 + - - -
297F VAL 4.1 0.2 - - - -
298F TYR* 3.8 9.9 - + - -
299F PRO* 3.3 41.0 - - + +
303F ALA 3.2 16.3 + - - +
304F GLU 3.2 0.4 + - - -
306F VAL* 1.3 79.9 - - - +
308F LEU* 1.3 92.2 + - + +
309F PRO* 3.5 4.0 - - - +
340G VAL* 4.2 7.6 - - + -
343G LEU* 3.6 25.1 - - + -
362G TYR* 4.7 2.9 + - - -
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Residues in contact with LEU 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F GLY 3.8 2.0 - - - -
121F GLY* 3.5 31.9 - - - +
261F GLU* 3.5 38.6 - - + +
298F TYR* 3.8 10.5 - - + +
304F GLU* 2.8 42.2 + - + +
305F SER* 4.5 4.6 - - - +
306F VAL 5.0 0.7 - - - -
307F TRP* 1.3 98.5 + - + +
309F PRO* 1.3 74.7 - - + +
310F ASN* 3.7 9.2 + - - +
313F ASP* 4.1 3.1 - - - +
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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