Contacts of the strand formed by residues 378 - 382 (chain A) in PDB entry 3DGR
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 ILE 378 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LYS* 2.6 33.9 + - - +
321A VAL* 3.8 36.1 - - + -
325A LEU* 5.8 1.3 - - + -
349A ARG* 6.3 0.2 - - - -
350A VAL* 3.3 25.6 - - + -
352A GLN* 4.3 6.7 - - + -
368A MET* 3.6 27.8 - - + -
375A ILE* 3.2 21.7 - - + +
376A GLU 3.3 0.6 - - - -
377A ASN* 1.3 78.4 - - - +
379A ALA* 1.3 73.6 + - - +
380A PHE* 3.8 28.5 - - + -
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Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A TYR 4.4 7.0 - - - +
189A LYS* 3.7 22.4 - - + +
309A ILE* 6.2 1.1 - - + -
350A VAL 3.0 7.9 + - - +
351A ILE* 3.3 17.4 - - + -
352A GLN 3.1 21.8 + - - -
378A ILE* 1.3 81.4 - - - +
380A PHE* 1.3 68.3 + - - +
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Residues in contact with PHE 380 (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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172A LEU* 3.9 26.7 - - + -
188A TYR 5.3 0.2 - - - +
189A LYS* 2.7 20.2 + - + +
190A LEU* 3.4 16.3 - - + -
191A HIS* 2.8 33.0 + - - +
351A ILE* 4.1 6.5 - - - +
352A GLN* 3.3 18.6 - - + +
356A VAL* 4.2 19.1 - - + -
361A LEU* 4.0 15.5 - - + -
364A ILE* 3.7 44.0 - - + -
365A VAL* 3.9 15.5 - - + -
378A ILE* 3.8 29.8 - - + -
379A ALA* 1.3 79.5 - - - +
381A GLY* 1.3 54.0 + - - +
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Residues in contact with GLY 381 (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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190A LEU* 4.6 0.7 - - - -
191A HIS 3.4 8.1 - - - -
193A PHE* 3.7 19.7 - - - -
351A ILE* 4.1 2.6 - - - +
352A GLN 2.9 9.4 + - - -
353A GLY* 3.3 25.5 - - - +
356A VAL* 3.4 16.7 - - - +
380A PHE* 1.3 73.5 - - - +
382A SER* 1.3 59.7 + - - -
501A A12 4.2 5.2 - - - -
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Residues in contact with SER 382 (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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168A GLN* 4.9 2.2 + - - -
190A LEU* 3.9 18.8 - - - +
191A HIS 3.0 8.7 + - - +
192A ASP* 3.8 3.6 - - - -
193A PHE* 2.9 21.7 + - - -
194A GLY 3.7 0.9 + - - -
353A GLY 5.1 0.2 - - - -
356A VAL* 2.7 31.1 + - - +
357A ASP* 4.5 1.0 - - - -
381A GLY* 1.3 74.8 - - - -
383A GLY* 1.3 61.0 + - - +
385A GLY 3.7 1.0 - - - -
386A LEU* 3.2 33.3 + - - +
501A A12 3.9 4.5 + - - -
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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