Contacts of the helix formed by residues 299 - 305 (chain C) in PDB entry 3ELP
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 GLN 299 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C SER* 5.3 3.0 - - - -
165C LYS* 3.6 7.9 - - - +
166C VAL* 2.6 50.2 + - + +
297C HIS* 3.0 18.7 + - + +
298C PRO* 1.3 113.7 - - + +
300C HIS* 1.3 63.3 + - - +
301C GLU* 3.1 4.0 - - - +
302C LEU* 3.1 19.9 + - + +
303C VAL* 3.1 21.3 + - - +
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Residues in contact with HIS 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PHE* 4.3 9.2 - + - -
292C PRO 2.9 20.8 + - - -
293C GLY 3.2 25.1 - - - -
294C LEU 3.3 13.9 + - - +
295C PRO* 3.3 29.5 - - + +
297C HIS* 2.9 20.2 + - + +
298C PRO 3.4 1.2 + - - -
299C GLN* 1.3 76.4 - - - +
301C GLU* 1.3 75.6 + - + +
303C VAL* 3.4 7.0 - - - +
304C LYS* 3.2 51.9 + - + +
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Residues in contact with GLU 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLU* 3.2 36.5 - - - +
288B LYS* 4.7 22.5 - - + +
298C PRO 5.2 0.6 + - - -
299C GLN* 3.1 1.5 - - - -
300C HIS* 1.3 83.7 - - + +
302C LEU* 1.3 67.7 + - - +
303C VAL 3.4 0.2 + - - -
304C LYS* 3.0 32.7 + - - +
305C ARG* 3.3 29.6 + - - +
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Residues in contact with LEU 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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166C VAL* 3.8 26.0 - - + +
167C ILE 3.9 0.7 - - - -
168C ASP* 3.6 45.3 - - + +
299C GLN* 3.1 21.1 + - + +
301C GLU* 1.3 77.4 - - - +
303C VAL* 1.3 68.4 + - - +
305C ARG* 2.9 39.2 + - + +
306C GLN* 3.1 33.4 + - + +
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Residues in contact with VAL 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PHE* 3.4 26.7 - - + -
166C VAL* 4.2 20.6 - - + +
292C PRO* 4.0 30.1 - - + +
297C HIS* 4.6 0.7 - - + -
299C GLN 3.2 15.7 - - - +
300C HIS* 3.4 15.7 - - - +
302C LEU* 1.3 76.5 - - - +
304C LYS* 1.3 57.4 + - - +
306C GLN* 2.6 26.5 + - - -
307C CYS* 2.8 32.6 + - + -
310C CYS* 4.3 9.0 - - - -
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Residues in contact with LYS 304 (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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286B VAL 5.1 0.8 + - - -
287B GLU* 3.4 29.2 + - - -
319B LYS* 4.1 9.5 - - - +
9C GLN* 5.1 1.1 - - - -
10C GLY* 3.4 36.0 - - - +
11C PHE* 3.2 22.0 - - + +
12C LEU* 3.0 27.9 + - - +
300C HIS* 3.2 38.3 + - + +
301C GLU* 3.0 35.7 + - - +
303C VAL* 1.3 78.9 - - - +
305C ARG* 1.3 58.1 + - - +
306C GLN 3.5 0.5 + - - -
307C CYS 3.6 0.3 - - - +
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Residues in contact with ARG 305 (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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12C LEU* 3.5 20.3 - - + +
168C ASP* 2.9 27.3 + - - -
170C GLU* 6.3 0.2 - - - +
201C LEU* 4.4 8.3 - - - +
301C GLU* 3.3 13.7 + - - +
302C LEU* 2.9 44.6 + - + +
303C VAL 2.8 1.8 + - - -
304C LYS* 1.3 74.9 - - - +
306C GLN* 1.3 56.1 + - - +
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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