Contacts of the helix formed by residues 343 - 350 (chain A) in PDB entry 2DOU
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 ARG 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A PRO* 4.2 7.4 - - - +
6A GLU* 4.9 13.4 + - - +
9A VAL* 4.4 23.4 - - + +
324A ASP* 2.5 31.3 + - - +
325A ASP* 2.9 33.0 + - - +
326A LEU* 4.8 10.4 - - - +
341A PRO* 4.5 0.4 - - + +
342A GLY* 1.3 76.1 - - - +
344A GLY* 1.3 61.1 + - - +
345A PHE 3.1 1.4 + - - -
346A GLY* 3.2 22.0 + - - +
347A PRO* 6.0 0.7 - - + -
349A GLY 3.1 7.2 + - - +
350A LYS* 3.7 46.7 - - + +
351A GLY 4.9 0.6 - - - +
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Residues in contact with GLY 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 3.6 21.2 - - - +
6A GLU 5.7 0.2 - - - -
9A VAL* 3.7 21.2 - - - +
10A PHE* 3.8 24.3 - - - -
122A PRO* 4.0 9.0 - - - +
341A PRO 2.7 20.5 + - - -
343A ARG* 1.3 72.9 - - - +
345A PHE* 1.3 59.6 + - - -
346A GLY 3.4 0.2 - - - -
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Residues in contact with PHE 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 4.9 0.2 - - - -
10A PHE* 4.3 9.9 - + - -
119A VAL* 3.4 8.6 - - + -
120A ALA 2.9 44.2 + - - +
121A TYR* 4.5 1.6 - + - -
122A PRO* 3.5 22.0 - - + -
125A PHE* 3.5 9.1 - - - -
169A ASN* 3.9 3.6 - - - -
170A PRO* 3.4 39.0 - - + -
316A TRP* 3.8 5.8 - + - -
340A ALA* 4.0 15.0 - - + -
341A PRO 4.0 9.0 - - - -
342A GLY 2.9 15.8 + - - +
344A GLY* 1.3 76.9 - - - +
346A GLY* 1.3 58.4 + - - +
354A ARG* 3.4 55.6 - - + -
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Residues in contact with GLY 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 4.1 11.1 - - - +
118A GLU 3.4 4.0 - - - -
125A PHE* 4.4 7.2 - - - -
343A ARG* 3.2 17.8 + - - +
344A GLY 3.4 1.4 - - - -
345A PHE* 1.3 81.1 - - - +
347A PRO* 1.3 65.4 - - - +
348A GLY 3.3 2.9 - - - -
349A GLY* 2.8 29.5 + - - -
350A LYS 4.3 0.2 + - - -
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Residues in contact with PRO 347 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A GLU* 3.5 13.2 - - + +
125A PHE* 5.2 1.6 - - + -
137A LEU* 3.4 32.3 - - + -
343A ARG* 6.0 1.1 - - + -
346A GLY* 1.3 77.1 - - - +
348A GLY* 1.3 57.6 + - - +
349A GLY 2.9 9.0 + - - -
350A LYS* 3.3 37.7 + - + +
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Residues in contact with GLY 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLU* 3.2 32.1 + - - +
119A VAL* 3.5 22.6 - - - +
316A TRP* 4.7 0.7 - - - -
346A GLY 3.2 0.4 + - - -
347A PRO* 1.3 77.6 - - - +
349A GLY* 1.3 58.3 + - - +
350A LYS 3.4 1.4 + - - +
352A PHE* 3.7 18.7 - - - -
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Residues in contact with GLY 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A VAL* 3.8 3.0 - - - +
316A TRP* 4.1 15.0 - - - -
342A GLY* 3.1 34.4 - - - -
343A ARG* 3.1 2.3 + - - -
346A GLY 2.8 15.5 + - - -
348A GLY* 1.3 79.2 - - - +
350A LYS* 1.3 63.0 + - - +
351A GLY 3.3 0.3 + - - -
352A PHE* 3.2 14.8 + - - +
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Residues in contact with LYS 350 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A ASP* 3.7 6.5 - - - -
343A ARG* 3.7 43.2 - - + +
346A GLY 4.3 0.4 + - - -
347A PRO* 3.3 30.3 - - + +
348A GLY 3.4 1.9 - - - +
349A GLY* 1.3 75.6 - - - +
351A GLY* 1.3 58.9 + - - +
352A PHE* 3.2 17.8 - - - -
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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