Contacts of the helix formed by residues 304 - 311 (chain A) in PDB entry 4DUB
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 SER 304 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A HIS* 3.3 7.4 - - - -
300A ASP* 5.3 3.1 - - - -
302A VAL 3.6 1.4 + - - -
303A PRO* 1.3 73.9 - - - +
305A TYR* 1.3 64.3 + - - +
306A LYS* 3.5 10.3 + - - +
307A GLN* 2.9 41.5 + - - +
308A VAL* 3.2 22.7 + - - +
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Residues in contact with TYR 305 (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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109A GLN* 2.7 46.3 + - - +
110A GLN* 5.0 0.5 + - - -
112A MET* 3.9 14.4 - - + -
113A LYS* 3.7 54.4 - - + +
116A HIS* 3.3 26.0 + - + -
304A SER* 1.3 72.9 - - - +
306A LYS* 1.3 72.0 + - + +
308A VAL* 3.2 13.3 + - - +
309A LYS* 3.2 32.0 + - + +
408A HIS* 3.4 24.7 - + - -
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Residues in contact with LYS 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A SER* 3.7 9.6 - - - +
305A TYR* 1.3 89.5 - - + +
307A GLN* 1.3 64.9 + - + +
309A LYS* 3.2 17.6 + - - +
310A GLN* 3.3 17.0 + - - +
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Residues in contact with GLN 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A VAL* 3.4 37.8 + - + +
298A LEU* 3.8 18.1 - - + +
299A VAL* 4.2 12.0 - - - +
300A ASP* 2.9 33.8 + - - +
302A VAL 4.0 1.2 - - - +
303A PRO* 3.3 9.7 - - - +
304A SER* 2.9 38.8 + - - +
306A LYS* 1.3 78.1 - - + +
308A VAL* 1.3 59.4 + - - +
310A GLN* 2.9 19.8 + - - -
311A LEU* 3.3 8.9 + - - +
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Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A HIS* 3.8 8.5 - - + -
303A PRO* 4.2 7.0 - - + -
304A SER 3.2 15.1 + - - +
305A TYR 3.2 7.4 + - - +
307A GLN* 1.3 75.8 - - - +
309A LYS* 1.3 63.1 + - + +
311A LEU* 3.1 27.4 + - + +
408A HIS* 3.7 24.5 - - + +
411A THR* 3.6 28.2 - - + +
412A LEU* 3.7 44.0 - - + +
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Residues in contact with LYS 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLN* 3.4 41.9 + - - +
305A TYR* 3.2 38.3 + - + +
306A LYS* 3.2 10.5 + - - +
308A VAL* 1.3 77.1 + - + +
310A GLN* 1.3 72.6 + - - +
311A LEU* 3.3 2.0 + - - -
312A LYS* 4.6 4.9 + - - +
408A HIS* 4.5 8.5 + - - +
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Residues in contact with GLN 310 (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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293A GLU* 4.0 4.0 - - - +
297A VAL* 3.9 25.4 - - + +
306A LYS 3.7 11.6 + - - +
307A GLN* 2.9 13.1 + - - +
309A LYS* 1.3 88.6 + - - +
311A LEU* 1.3 57.7 + - - +
312A LYS* 2.9 15.7 + - - +
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Residues in contact with LEU 311 (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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293A GLU* 3.2 18.2 - - + +
294A ALA* 4.2 20.0 - - + -
297A VAL* 3.6 28.0 - - + -
298A LEU* 4.3 15.0 - - + -
307A GLN 3.6 8.3 - - - +
308A VAL* 3.1 24.2 + - + +
309A LYS 3.3 2.6 - - - -
310A GLN* 1.3 73.8 - - - +
312A LYS* 1.3 63.6 + - - +
314A VAL* 3.3 11.5 + - + -
315A GLY* 3.0 17.7 + - - -
411A THR* 3.7 34.7 - - + +
412A LEU* 5.1 0.9 - - - -
415A GLY* 4.2 13.2 - - - -
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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