Contacts of the helix formed by residues 297 - 302 (chain C) in PDB entry 1ML3
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 VAL 297 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C GLU 4.7 0.2 - - - +
296C LEU* 1.3 79.5 - - - +
298C SER* 1.3 68.2 + - - +
299C ALA 4.2 0.7 - - - +
300C ASP* 2.7 26.0 + - - +
301C PHE* 3.7 4.5 - - - -
332C TRP* 4.1 5.4 - - - -
212D ARG* 4.0 26.2 - - + +
215D ARG* 3.4 39.9 - - + +
220D ASN* 3.7 21.5 - - + +
221D ILE 3.8 9.6 - - - +
222D ILE* 3.8 25.8 - - + -
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Residues in contact with SER 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C THR* 4.8 2.6 - - - +
254C ASP 4.9 2.9 - - - -
255C VAL* 3.3 32.4 - - - +
297C VAL* 1.3 70.7 - - - +
299C ALA* 1.3 68.6 + - - -
301C PHE* 3.0 13.5 + - - -
332C TRP* 3.4 24.7 - - - -
219D VAL 3.8 3.1 + - - -
220D ASN* 3.1 12.0 + - - -
221D ILE* 2.9 44.4 + - - +
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Residues in contact with ALA 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASP 5.6 0.4 - - - -
54A THR* 3.7 38.7 - - + +
58A LYS* 5.7 0.5 - - - -
297C VAL 2.9 2.6 + - - -
298C SER* 1.3 79.0 + - - +
300C ASP* 1.3 61.7 + - - +
301C PHE 3.3 1.0 + - - -
302C ILE* 3.3 34.0 + - + +
215D ARG* 4.4 2.9 - - - +
219D VAL 5.0 2.2 - - - +
220D ASN* 3.0 19.6 + - - +
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Residues in contact with ASP 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR* 3.4 19.0 - - + +
53A ASP 4.3 2.4 + - - +
58A LYS* 3.2 32.8 + - - +
296C LEU* 3.2 38.0 - - + +
297C VAL 2.7 33.3 + - - +
299C ALA* 1.3 70.7 - - - +
301C PHE* 1.3 59.5 + - + +
302C ILE 3.4 0.4 - - - -
215D ARG* 2.7 45.8 + - - -
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Residues in contact with PHE 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C VAL* 4.0 13.0 - - + -
292C THR* 4.1 5.4 - - + -
296C LEU* 3.6 42.0 - - + -
297C VAL 3.7 12.8 - - - -
298C SER 3.0 10.9 + - - +
300C ASP* 1.3 77.6 - - - +
302C ILE* 1.3 64.8 - - - +
303C ASN 3.0 3.6 + - - -
304C ASP* 3.1 27.5 + - + +
309C ILE* 3.5 42.8 - - + -
332C TRP* 3.3 58.1 - + + -
333C TYR 5.1 0.2 - - - +
334C ASP* 3.6 15.0 - - - +
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Residues in contact with ILE 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A THR 5.3 4.9 - - - +
58A LYS* 4.8 8.8 + - - -
55C VAL* 3.4 36.3 - - + +
56C HIS* 4.2 5.4 - - + +
253C PRO* 6.2 3.6 - - + -
254C ASP* 5.0 7.2 - - + +
255C VAL* 3.5 19.3 - - + -
299C ALA* 3.3 34.6 + - + +
300C ASP 3.4 2.5 - - - +
301C PHE* 1.3 75.5 - - - +
303C ASN* 1.3 84.6 + - - +
334C ASP* 3.5 8.7 - - - +
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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
------------------------------------------------------------
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