Contacts of the helix formed by residues 385 - 394 (chain A) in PDB entry 3QFR
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 ARG 385 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A THR* 4.2 25.4 + - - +
96A GLU* 3.2 40.0 + - - +
97A PHE* 3.9 12.3 - - - -
100A ARG* 3.8 9.9 - - - +
215A LEU* 6.0 0.6 - - - +
216A GLU* 2.8 37.6 - - + +
379A ASP* 5.8 0.2 + - - -
383A PRO 3.6 4.7 + - - +
384A PRO* 1.3 76.3 - - - +
386A THR* 1.3 63.1 + - - +
387A ASN* 3.4 12.6 - - - +
388A VAL* 3.1 19.1 + - + +
389A LEU* 3.3 10.4 + - - +
419A TYR* 3.3 5.8 - - - +
452A PRO* 4.2 14.9 - - - +
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Residues in contact with THR 386 (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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100A ARG* 3.6 10.9 + - - -
216A GLU* 2.5 36.3 + - + +
217A GLU* 4.2 0.2 - - - +
220A ILE* 3.6 25.0 - - + +
223A ARG* 5.5 0.7 + - - -
385A ARG* 1.3 70.7 - - - +
387A ASN* 1.3 64.2 + - - -
389A LEU* 2.9 24.7 + - - +
390A TYR* 3.0 12.4 + - - +
408A MET 4.0 12.6 - - - +
409A ALA* 4.1 22.1 + - - +
419A TYR* 3.7 23.7 + - + -
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Residues in contact with ASN 387 (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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96A GLU* 5.3 3.6 + - - -
100A ARG* 2.9 59.6 - - + +
223A ARG* 6.2 1.8 - - - +
385A ARG* 4.0 10.5 - - - +
386A THR* 1.3 80.6 + - - +
388A VAL* 1.3 74.4 + - - +
390A TYR* 3.6 7.2 + - - +
391A GLU* 3.0 40.1 + - - +
409A ALA* 5.8 0.4 - - - -
450A LEU* 5.1 2.9 - - - +
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Residues in contact with VAL 388 (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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96A GLU* 5.9 2.5 - - - +
384A PRO* 4.3 18.4 - - + -
385A ARG* 3.1 16.7 + - + +
386A THR 3.0 1.0 - - - -
387A ASN* 1.3 92.9 + - - +
389A LEU* 1.3 67.3 + - + +
390A TYR 3.1 0.6 + - - -
391A GLU* 3.6 6.4 + - - +
392A LEU* 3.4 35.3 + - + +
430A ILE* 5.5 1.1 - - + -
447A LEU* 5.6 0.9 - - + -
450A LEU* 3.5 43.9 - - + +
451A LEU* 5.0 12.1 - - + -
452A PRO* 5.5 4.3 - - + -
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Residues in contact with LEU 389 (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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384A PRO* 4.3 10.1 - - + +
385A ARG 3.3 6.9 + - - +
386A THR* 2.9 9.2 + - - +
388A VAL* 1.3 77.9 - - - +
390A TYR* 1.3 63.5 + - - +
392A LEU* 3.6 11.9 + - + +
393A ALA* 3.4 16.3 + - - +
405A LEU* 4.2 29.8 - - + +
408A MET* 3.6 31.4 - - + -
409A ALA* 6.2 0.4 - - + -
419A TYR* 3.5 39.5 - - + -
423A VAL* 3.8 4.3 - - + -
433A ILE* 3.4 34.1 - - + -
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Residues in contact with TYR 390 (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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242A GLU* 4.7 20.0 + - + +
244A SER* 5.8 7.6 - - - -
386A THR 3.0 11.1 + - - +
387A ASN* 3.7 12.1 - - - +
388A VAL 3.1 0.2 - - - -
389A LEU* 1.3 74.6 - - - +
391A GLU* 1.3 85.1 + - - +
393A ALA* 2.9 23.5 + - - +
394A GLN 4.3 0.9 + - - -
405A LEU 5.3 2.7 - - - -
406A ARG* 3.1 51.1 + - - +
409A ALA* 3.8 25.1 - - + +
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Residues in contact with GLU 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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244A SER* 3.2 29.8 - - - -
245A ILE 4.7 3.1 + - - +
387A ASN* 3.0 27.2 + - - +
388A VAL 3.6 2.0 + - - +
390A TYR* 1.3 89.9 - - - +
392A LEU* 1.3 57.3 - - - +
394A GLN* 3.0 35.7 - - - +
395A TYR* 3.9 3.9 - - - -
446A HIS* 4.3 10.2 + - - +
450A LEU* 3.5 35.6 - - + +
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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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388A VAL* 3.4 24.5 + - + +
389A LEU* 4.0 12.8 - - + +
390A TYR 3.1 1.4 - - - -
391A GLU* 1.3 74.7 - - - +
393A ALA* 1.3 64.4 + - - +
394A GLN 3.2 3.4 - - - -
395A TYR* 3.1 18.6 + - + +
405A LEU* 4.6 2.0 - - + -
430A ILE* 3.8 28.7 - - + -
433A ILE* 5.6 3.4 - - + -
434A LEU* 5.0 3.1 - - + -
440A LEU* 3.1 32.6 - - + +
442A PRO* 3.8 29.8 - - + -
447A LEU* 4.0 18.2 - - + +
450A LEU* 4.1 17.3 - - + -
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Residues in contact with ALA 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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389A LEU 3.4 9.0 + - - +
390A TYR 2.9 15.9 + - - +
392A LEU* 1.3 77.7 - - - +
394A GLN* 1.3 56.4 + - - +
395A TYR 3.1 0.2 - - - -
396A ALA* 3.0 26.3 + - - +
402A GLN* 3.3 13.6 - - + +
405A LEU* 4.0 21.5 - - + -
406A ARG* 3.7 35.4 - - + +
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Residues in contact with GLN 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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244A SER* 3.6 25.7 - - - -
390A TYR 4.3 0.8 + - - +
391A GLU* 3.0 24.3 + - - +
393A ALA* 1.3 77.0 - - - +
395A TYR* 1.3 93.3 + - + +
396A ALA 3.2 5.0 + - - -
402A GLN* 5.1 6.6 - - - +
446A HIS* 5.0 3.4 + - - -
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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