Contacts of the helix formed by residues 390 - 401 (chain A) in PDB entry 4QGC
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 390 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ASP* 2.7 38.2 + - - -
25A THR* 3.4 20.7 + - - -
26A PHE* 3.6 40.1 - + + -
29A HIS* 4.0 26.0 - + + -
388A ALA 3.5 2.6 + - - -
389A ILE* 1.3 69.9 - - - +
391A HIS* 1.3 65.9 + - - +
392A LEU* 3.4 11.4 + - + +
393A GLN* 3.5 46.4 + - + -
394A LEU* 3.2 22.1 - - + +
397D GLU* 4.7 1.6 - - - -
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Residues in contact with HIS 391 (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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44A ASN* 5.8 3.2 + - - -
386A GLU* 4.7 8.1 - - + -
389A ILE* 3.4 27.1 + - + -
390A TYR* 1.3 73.8 - - - +
392A LEU* 1.3 63.7 + - - +
394A LEU* 3.3 26.7 + - + +
395A PHE* 3.4 5.0 + - - +
421A PHE* 4.1 12.5 - - + -
445A ARG 3.9 11.1 - - - +
446A PRO 3.7 9.8 + - - -
447A ARG* 3.6 61.6 + - + +
467A ARG* 3.0 31.7 + - - -
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Residues in contact with LEU 392 (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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390A TYR* 3.4 13.4 + - + +
391A HIS* 1.3 78.5 - - - +
393A GLN* 1.3 57.6 + - - +
395A PHE* 3.4 11.1 + - + -
396A GLU* 3.0 55.4 + - - +
421A PHE* 3.6 45.5 - - + -
447A ARG* 6.1 0.9 - - - +
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Residues in contact with GLN 393 (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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26A PHE* 4.8 2.9 - - - +
390A TYR* 3.5 37.0 + - + +
391A HIS 3.3 0.6 - - - -
392A LEU* 1.3 75.3 - - - +
394A LEU* 1.3 71.1 + - + +
396A GLU* 4.5 6.3 - - - -
397A GLU* 3.0 51.6 + - + +
26D PHE* 3.9 14.7 - - - +
393D GLN* 2.7 40.7 + - - +
397D GLU* 4.6 1.8 + - - -
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Residues in contact with LEU 394 (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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389A ILE* 4.1 24.0 - - + -
390A TYR* 3.2 20.9 - - + +
391A HIS* 3.3 15.7 - - + +
393A GLN* 1.3 84.4 - - + +
395A PHE* 1.3 57.5 + - - +
397A GLU* 3.8 4.0 - - - +
398A LEU* 2.9 44.0 + - + +
445A ARG* 4.2 33.4 - - + +
467A ARG* 5.6 2.2 - - - +
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Residues in contact with PHE 395 (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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391A HIS 3.4 4.9 + - - +
392A LEU* 3.8 15.0 - - + +
393A GLN 3.3 0.4 - - - -
394A LEU* 1.3 78.1 - - - +
396A GLU* 1.3 63.5 + - + +
398A LEU* 3.2 2.3 + - - -
399A ARG* 3.0 54.6 + - + +
414A VAL* 4.1 7.2 - - + -
417A VAL* 3.6 24.5 - - + -
418A GLU* 3.6 50.0 - - + -
421A PHE* 3.9 28.5 - + + -
444A TYR* 3.4 36.6 - + + +
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Residues in contact with GLU 396 (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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392A LEU* 3.0 47.5 + - + +
393A GLN* 4.0 6.4 - - - +
395A PHE* 1.3 78.3 - - + +
397A GLU* 1.3 61.7 + - + +
399A ARG* 3.8 29.4 + - - +
400A ARG* 3.5 22.0 + - - +
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Residues in contact with GLU 397 (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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393A GLN* 3.0 42.3 + - + +
394A LEU* 3.9 3.8 - - - +
396A GLU* 1.3 75.2 - - + +
398A LEU* 1.3 62.3 + - - +
399A ARG 3.1 4.9 - - - -
400A ARG* 4.0 1.4 - - - +
401A LEU* 3.2 28.9 + - - +
25D THR* 3.4 23.1 - - + +
26D PHE* 2.9 27.2 + - - +
27D LEU* 2.9 38.6 + - + +
390D TYR* 4.4 4.7 - - - -
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Residues in contact with LEU 398 (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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318A ASN* 3.6 28.5 - - + +
319A ARG* 4.4 4.7 - - + -
394A LEU* 2.9 32.6 + - + +
395A PHE* 3.2 4.9 + - - +
397A GLU* 1.3 76.6 - - + +
399A ARG* 1.3 57.4 + - - +
401A LEU 4.5 2.0 - - - -
402A ALA* 3.2 25.3 - - - +
443A ARG* 3.2 33.2 + - - +
444A TYR* 3.7 23.3 - - + -
445A ARG* 3.8 19.1 - - + -
27D LEU* 3.7 26.9 - - + -
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Residues in contact with ARG 399 (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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395A PHE* 3.0 37.3 + - + +
396A GLU* 3.8 34.7 + - - +
397A GLU 3.1 0.2 - - - -
398A LEU* 1.3 79.1 - - - +
400A ARG* 1.3 63.2 + - - +
401A LEU 3.6 0.2 - - - -
402A ALA* 4.2 8.5 + - - +
414A VAL* 4.1 15.3 - - + -
418A GLU* 2.2 40.0 + - - -
444A TYR* 4.5 6.5 - - + -
418B GLU* 4.2 2.8 + - - -
422B ARG* 3.5 26.6 - - - +
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Residues in contact with ARG 400 (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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396A GLU 3.5 15.3 + - - +
397A GLU 3.4 3.9 + - - +
399A ARG* 1.3 83.1 - - - +
401A LEU* 1.3 78.6 + - + +
402A ALA 3.4 4.7 + - - +
25D THR* 3.4 39.8 - - - +
390D TYR* 5.3 2.0 + - - -
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Residues in contact with LEU 401 (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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319A ARG* 4.5 20.6 - - + +
397A GLU 3.2 14.2 + - - +
398A LEU* 4.5 1.8 - - - +
400A ARG* 1.3 116.1 - - + +
402A ALA* 1.3 58.3 + - - +
403A PRO* 4.6 0.7 - - - +
443A ARG* 5.5 0.7 + - - -
25D THR* 4.2 8.1 - - + +
27D LEU* 5.5 5.3 - - + +
28D GLU* 3.3 41.1 - - + +
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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