Contacts of the helix formed by residues 301 - 307 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299I THR 3.5 5.3 + - - +
300I THR* 1.3 71.1 - - - +
302I TRP* 1.3 64.1 + - - +
303I ILE* 3.4 11.6 + - - +
304I ALA* 3.1 31.4 + - + +
305I ILE* 3.1 24.0 + - - +
310I VAL* 5.2 4.6 - - + +
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Residues in contact with TRP 302 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148I ALA* 3.5 29.8 - - + -
151I VAL* 3.8 26.9 - - + -
152I LEU* 3.6 36.7 - - + +
292I LYS* 3.3 62.0 + - + +
297I PHE* 3.7 38.2 + + + -
300I THR* 3.7 25.2 + - + +
301I ASP* 1.3 71.6 + - - +
303I ILE* 1.3 72.2 + - + +
305I ILE* 3.5 2.8 + - + +
306I TYR* 3.1 17.8 + - - +
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Residues in contact with ILE 303 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I GLU* 4.9 25.1 - - + +
15I VAL* 6.3 3.4 - - + -
301I ASP* 3.3 8.6 - - - +
302I TRP* 1.3 84.7 - - + +
304I ALA* 1.3 61.2 + - - +
306I TYR* 3.2 10.3 + - + +
307I GLN* 2.9 56.5 + - + +
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Residues in contact with ALA 304 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301I ASP* 3.1 31.4 + - + +
303I ILE* 1.3 79.8 - - - +
305I ILE* 1.3 57.3 + - - +
307I GLN* 3.4 5.3 + - - -
308I ARG 3.0 6.9 + - - -
309I LYS* 2.8 42.9 + - + -
310I VAL* 3.7 19.3 - - + +
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Residues in contact with ILE 305 (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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102I PHE* 3.4 11.2 - - + -
145I PHE* 5.0 11.0 - - + +
148I ALA* 3.2 16.4 - - + -
149I GLN* 3.8 31.2 - - + +
152I LEU* 4.1 14.4 - - + -
179I TYR* 3.6 9.0 - - + -
300I THR* 3.1 36.1 - - + -
301I ASP 3.1 11.1 + - - +
302I TRP* 3.6 8.3 - - + +
304I ALA* 1.3 73.4 - - - +
306I TYR* 1.3 61.3 + - - +
308I ARG* 2.9 19.8 + - - +
310I VAL* 3.9 20.6 - - + -
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Residues in contact with TYR 306 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I PHE* 3.4 30.9 - + - -
100I PHE* 3.6 28.5 - + - -
101I PRO* 3.6 42.2 - - + +
102I PHE* 3.9 9.2 - + - -
152I LEU* 4.1 8.3 - - + +
302I TRP 3.1 14.0 + - - +
303I ILE* 3.2 12.1 + - + +
305I ILE* 1.3 77.2 - - - +
307I GLN* 1.3 73.3 + - + +
308I ARG* 3.3 11.1 + - - +
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Residues in contact with GLN 307 (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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303I ILE* 2.9 40.2 + - - +
304I ALA* 4.0 5.1 - - - +
305I ILE 3.2 0.2 - - - -
306I TYR* 1.3 87.0 - - + +
308I ARG* 1.3 69.8 + - - +
309I LYS* 2.9 47.7 + - + +
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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