Contacts of the helix formed by residues 378 - 385 (chain A) in PDB entry 3Q0F
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 TYR 378 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376A PHE* 3.6 2.2 - - - +
377A GLN* 1.3 122.1 + - + +
379A ARG* 1.3 63.5 + - - +
380A MET* 3.0 10.0 + - + +
381A GLU* 2.5 41.7 + - + +
382A LEU* 3.7 7.6 + - - +
485A ASN* 5.5 0.7 - - - -
486A TYR* 4.1 5.8 - - - -
8B G 3.4 40.2 - - - +
9B T 2.4 27.3 + - - -
380X MET* 3.5 31.2 - - + -
383X ASN* 3.7 8.4 + - - -
384X LEU* 3.5 30.7 - - + -
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Residues in contact with ARG 379 (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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378A TYR* 1.3 71.1 - - - +
380A MET* 1.3 64.0 + - + +
382A LEU* 3.4 34.9 - - - +
383A ASN* 3.5 5.7 + - - +
388A HIS* 3.5 10.9 + - - +
390A PRO 3.4 20.7 + - - +
391A SER* 3.5 20.4 + - - +
392A GLN 3.0 25.0 + - - +
393A SER 2.7 29.3 + - - -
411A VAL* 4.0 18.6 - - - +
413A SER* 5.0 0.6 + - - -
486A TYR* 3.5 28.7 + - - +
6B G 3.8 14.1 + - - +
7B A 3.3 35.0 - - - +
8B G 2.7 12.8 + - - +
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Residues in contact with MET 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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378A TYR* 3.0 2.9 + - + +
379A ARG* 1.3 79.1 - - + +
381A GLU* 1.3 65.8 + - - +
382A LEU 3.1 1.3 - - - -
383A ASN* 2.9 27.3 + - + +
384A LEU* 2.9 30.2 + - + +
391A SER* 3.6 35.4 - - - -
8B G 5.9 0.7 - - - +
7C T 4.5 9.0 - - - +
8C C 5.0 0.4 - - - +
378X TYR* 3.4 55.9 - - + -
380X MET* 4.1 34.1 - - + -
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Residues in contact with GLU 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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376A PHE* 3.5 21.7 - - + -
377A GLN* 2.6 26.6 + - - +
378A TYR* 2.5 48.2 + - + +
380A MET* 1.3 77.0 - - - +
382A LEU* 1.3 61.1 + - - +
384A LEU* 3.2 13.0 + - + +
385A LEU* 3.2 31.4 + - + +
384X LEU* 4.6 19.2 - - + +
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Residues in contact with LEU 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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376A PHE* 3.5 42.6 - - + -
378A TYR 3.9 5.8 - - - +
379A ARG* 3.4 36.3 - - - +
380A MET 3.1 0.2 - - - -
381A GLU* 1.3 75.8 - - - +
383A ASN* 1.3 60.2 - - - +
385A LEU 3.6 0.5 + - - -
386A GLY 3.2 2.1 + - - -
387A ILE* 2.8 44.6 + - + +
388A HIS* 3.2 24.6 + - + +
411A VAL* 4.4 2.7 - - + -
469A ILE* 4.1 32.5 - - + -
486A TYR* 4.7 6.7 - - + -
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Residues in contact with ASN 383 (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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379A ARG 3.5 1.5 + - - +
380A MET* 2.9 40.4 + - + +
382A LEU* 1.3 76.3 - - - +
384A LEU* 1.3 63.4 + - + +
385A LEU 3.1 2.0 - - - -
386A GLY* 2.9 20.1 + - - -
388A HIS 3.2 14.7 + - - +
389A ARG* 2.7 37.3 + - - +
8C C 3.7 8.7 + - - -
377X GLN* 5.2 0.3 - - - +
378X TYR* 3.7 20.5 + - - -
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Residues in contact with LEU 384 (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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380A MET* 2.9 20.0 + - + +
381A GLU* 3.2 14.3 + - + +
383A ASN* 1.3 78.2 - - - +
385A LEU* 1.3 68.0 + - + +
386A GLY 3.4 0.2 - - - -
377X GLN* 3.8 13.7 - - - +
378X TYR* 3.7 32.1 - - + -
381X GLU* 4.5 25.4 - - + +
384X LEU* 6.3 3.6 - - + -
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Residues in contact with LEU 385 (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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363A ILE* 5.9 0.2 - - - +
367A VAL* 3.5 20.4 - - - +
370A VAL* 4.6 13.5 - - + -
376A PHE* 3.6 32.1 - - + -
381A GLU* 3.2 15.5 + - + +
383A ASN 3.1 0.6 - - - -
384A LEU* 1.3 86.2 - - + +
386A GLY* 1.3 62.8 + - - +
387A ILE* 3.3 18.4 - - + -
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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