Contacts of the helix formed by residues 301 - 307 (chain L) in PDB entry 3E8E
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 ASP 301 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299L THR 3.6 5.5 + - - +
300L THR* 1.3 70.8 - - - +
302L TRP* 1.3 59.3 + - - +
303L ILE* 3.6 12.1 + - - +
304L ALA* 2.9 47.5 + - + +
305L ILE* 3.0 16.0 + - - +
310L VAL* 5.1 4.0 - - + -
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Residues in contact with TRP 302 (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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148L ALA* 3.2 29.2 - - + -
151L VAL* 3.6 28.0 - - + -
152L LEU* 3.8 31.2 - - + +
292L LYS* 3.5 59.0 + - + +
297L PHE* 3.6 40.6 + + - -
300L THR* 3.3 27.4 + - + +
301L ASP* 1.3 72.8 + - - +
303L ILE* 1.3 63.4 + - + +
305L ILE* 3.5 4.6 + - + +
306L TYR* 3.1 27.4 + - - +
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Residues in contact with ILE 303 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301L ASP* 3.2 9.1 - - - +
302L TRP* 1.3 82.0 - - + +
304L ALA* 1.3 61.6 + - - +
306L TYR* 3.4 7.3 + - + +
307L GLN* 3.0 56.7 + - + +
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Residues in contact with ALA 304 (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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301L ASP* 2.9 35.0 + - + +
303L ILE* 1.3 80.4 - - - +
305L ILE* 1.3 58.2 + - - +
307L GLN* 3.5 4.0 + - - -
308L ARG 3.1 6.4 + - - -
309L LYS* 2.8 43.0 + - + +
310L VAL* 3.6 17.1 + - + -
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Residues in contact with ILE 305 (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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102L PHE* 3.3 11.4 - - + -
145L PHE* 4.6 15.7 - - + +
148L ALA* 3.4 17.5 - - + -
149L GLN* 3.8 30.7 - - + +
152L LEU* 3.9 13.9 - - + -
179L TYR* 3.7 8.9 - - + -
300L THR* 3.3 33.9 - - + +
301L ASP 3.0 13.2 + - - +
302L TRP* 3.8 7.4 - - - +
303L ILE 3.3 0.2 - - - -
304L ALA* 1.3 74.1 - - - +
306L TYR* 1.3 65.2 + - - +
308L ARG* 3.0 13.3 + - - -
310L VAL* 3.9 19.7 - - + -
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Residues in contact with TYR 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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18L PHE* 3.1 35.3 - + - -
100L PHE* 3.6 37.0 - + - -
101L PRO* 3.7 31.1 - - + +
102L PHE* 4.0 9.6 - + - -
152L LEU* 4.0 12.7 - - + +
302L TRP 3.1 18.0 + - - +
303L ILE* 3.6 7.6 - - + +
305L ILE* 1.3 76.3 - - - +
307L GLN* 1.3 75.0 + - + +
308L ARG* 3.4 8.8 + - - +
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Residues in contact with GLN 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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303L ILE* 3.0 41.2 + - - +
304L ALA* 4.0 2.3 - - - +
305L ILE 3.2 0.2 - - - -
306L TYR* 1.3 88.3 - - + +
308L ARG* 1.3 71.2 + - - +
309L LYS* 3.2 47.9 + - + +
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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