Contacts of the strand formed by residues 349 - 354 (chain A) in PDB entry 1D0N
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 349 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ARG 4.5 5.2 - - - +
121A GLU* 4.8 3.8 - - - +
125A PHE* 3.1 30.0 + - - +
126A GLU 3.7 10.1 + - - -
127A SER* 3.9 20.4 - - - +
313A GLY 3.3 17.7 + - - +
314A LYS* 3.2 35.6 + - + +
315A ILE 2.9 27.4 + - - +
347A GLN 3.4 2.2 + - - +
348A THR* 1.3 76.0 - - - +
350A VAL* 1.3 62.2 + - - +
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Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN 3.8 0.4 - - - +
119A HIS* 3.4 5.4 + - - +
120A ARG* 3.0 57.8 + - + +
315A ILE* 3.6 14.6 - - + +
317A VAL* 4.6 1.3 - - + -
332A LEU* 5.1 4.9 - - + -
335A ALA* 3.8 25.4 - - + -
339A ILE* 3.9 22.0 - - + -
348A THR 3.6 11.4 + - - +
349A GLN* 1.3 79.2 - - - +
351A SER* 1.3 70.5 + - - +
352A VAL* 4.3 14.6 - - + -
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Residues in contact with SER 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN 3.1 8.1 - - - -
119A HIS* 3.2 24.1 + - - -
314A LYS* 4.1 17.5 + - - -
315A ILE 3.3 6.2 + - - +
316A PHE* 3.4 18.2 - - - -
317A VAL* 2.8 25.3 + - - +
350A VAL* 1.3 74.9 + - - +
352A VAL* 1.3 63.6 + - - +
353A LEU* 3.9 17.9 - - - +
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Residues in contact with VAL 352 (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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116A ALA 4.3 0.4 - - - +
117A VAL* 3.7 3.1 - - - -
118A GLN* 2.9 62.1 + - + +
317A VAL* 3.1 32.1 - - + +
319A LYS* 4.3 15.7 - - + +
331A ALA* 4.5 10.1 - - + +
332A LEU* 3.6 26.2 - - + -
350A VAL* 4.3 5.6 - - + -
351A SER* 1.3 76.5 - - - +
353A LEU* 1.3 64.5 + - - +
354A PRO* 4.2 0.9 - - - +
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Residues in contact with LEU 353 (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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117A VAL* 3.5 21.8 - - + -
316A PHE* 4.4 7.2 - - + -
317A VAL 2.8 12.9 + - - +
318A TRP* 3.6 8.0 - - + -
319A LYS* 2.9 30.6 + - - +
351A SER* 3.9 14.6 - - - +
352A VAL* 1.3 87.4 - - - +
354A PRO* 1.3 71.4 - - + +
357A GLY 4.6 1.6 - - - +
358A GLU* 3.9 9.6 - - + -
359A THR* 3.7 24.5 - - + +
362A PHE* 3.5 44.2 - - + -
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Residues in contact with PRO 354 (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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114A GLY 4.0 15.3 - - - +
115A ARG* 4.3 17.7 - - - +
116A ALA 3.8 23.3 - - - +
117A VAL* 4.5 8.1 - - + -
318A TRP* 4.9 1.6 - - - -
319A LYS* 3.8 20.6 - - + +
352A VAL 4.2 0.4 - - - +
353A LEU* 1.3 89.5 - - + +
355A GLU* 1.3 70.7 + - - +
356A GLY 3.2 0.2 + - - -
357A GLY* 2.9 30.4 + - - +
358A GLU* 3.9 3.3 + - - +
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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