Contacts of the helix formed by residues 385 - 394 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B THR* 4.0 25.0 + - - +
96B GLU* 5.5 12.3 - - - +
97B PHE* 4.6 14.8 - - - -
100B ARG* 4.2 7.0 - - - +
211B ASP* 6.0 0.2 + - - -
215B LEU* 5.3 4.9 - - - +
216B GLU* 2.6 56.2 + - - +
383B PRO 4.6 4.9 - - - +
384B PRO* 1.3 77.3 - - - +
386B THR* 1.3 65.9 + - - +
387B ASN* 3.2 18.8 - - - +
388B VAL* 2.9 21.6 + - + +
389B LEU* 3.2 12.1 + - - +
419B TYR* 3.2 6.9 + - - +
452B PRO* 6.3 3.7 - - + +
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Residues in contact with THR 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ARG* 3.7 7.8 + - - -
216B GLU* 3.1 22.4 + - + +
217B GLU* 4.5 0.2 - - - +
220B ILE* 3.8 18.0 - - + +
385B ARG* 1.3 73.6 - - - +
387B ASN* 1.3 65.3 + - - +
389B LEU* 3.3 9.4 + - - +
390B TYR* 2.9 24.3 + - - +
408B MET 3.0 28.7 - - - +
409B ALA* 3.6 16.1 + - - +
419B TYR* 3.6 27.3 + - + -
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Residues in contact with ASN 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B GLU* 6.2 0.6 - - - +
100B ARG* 3.1 61.3 - - + +
103B LYS* 4.2 12.4 + - - +
223B ARG* 4.9 4.5 - - - +
385B ARG* 3.5 17.2 - - - +
386B THR* 1.3 83.1 + - - +
388B VAL* 1.3 75.5 + - - +
390B TYR* 3.5 7.3 - - - +
391B GLU* 3.3 30.2 + - + +
409B ALA* 5.6 0.9 - - - -
450B LEU* 5.3 4.7 - - - +
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Residues in contact with VAL 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B PRO* 4.3 14.6 - - + -
385B ARG* 2.9 22.6 + - + +
387B ASN* 1.3 92.8 - - - +
389B LEU* 1.3 65.8 + - - +
391B GLU* 3.6 2.4 + - - +
392B LEU* 3.1 37.4 + - + +
430B ILE* 5.4 0.7 - - + -
447B LEU* 5.3 1.6 - - + -
450B LEU* 3.6 46.2 - - + +
451B LEU* 5.2 9.4 - - + +
452B PRO* 5.4 6.1 - - + -
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Residues in contact with LEU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B PRO* 4.1 13.2 - - + -
385B ARG 3.2 10.2 + - - +
386B THR* 3.3 6.9 + - - +
388B VAL* 1.3 73.6 - - + +
390B TYR* 1.3 70.1 + - - +
392B LEU* 3.0 12.8 + - + +
393B ALA* 2.9 19.1 + - - +
405B LEU* 3.8 28.9 - - + +
408B MET* 3.9 27.8 - - + -
419B TYR* 3.8 32.1 - - + -
423B VAL* 4.0 5.6 - - + -
430B ILE* 5.6 0.7 - - + -
433B ILE* 3.5 31.9 - - + -
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Residues in contact with TYR 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ARG* 6.1 2.9 - - - -
243B SER 5.4 11.3 + - - -
386B THR 2.9 13.6 + - - +
387B ASN* 3.5 13.2 - - - +
389B LEU* 1.3 74.3 - - - +
391B GLU* 1.3 70.4 + - - +
393B ALA* 2.8 29.2 + - - +
394B GLN* 4.1 1.7 + - - +
405B LEU 3.8 6.2 + - - -
406B ARG* 3.4 50.2 + - + -
409B ALA* 4.4 14.4 - - + -
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Residues in contact with GLU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LYS* 4.2 10.5 + - - +
243B SER 5.4 3.1 + - - -
244B SER* 4.0 11.4 + - - -
245B ILE* 3.4 46.2 + - - +
387B ASN* 3.3 16.9 + - + +
388B VAL 4.0 1.6 - - - +
390B TYR* 1.3 88.9 - - + +
392B LEU* 1.3 60.7 + - - +
394B GLN* 3.1 31.0 - - - +
395B TYR* 4.0 3.8 - - - -
446B HIS* 4.4 8.9 + - - +
450B LEU* 3.8 31.9 - - + -
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B VAL* 3.1 27.2 + - + +
389B LEU* 3.0 11.9 + - + +
390B TYR 2.9 0.2 + - - -
391B GLU* 1.3 73.9 - - - +
393B ALA* 1.3 65.9 + - - +
394B GLN 3.1 3.1 - - - -
395B TYR* 2.9 21.9 + - + -
405B LEU* 4.8 0.7 - - + -
430B ILE* 4.0 17.9 - - + -
433B ILE* 6.2 0.2 - - + -
434B LEU* 5.6 1.6 - - + -
440B LEU* 3.2 30.7 - - + +
442B PRO* 3.9 30.3 - - + -
446B HIS* 4.9 0.9 - - + -
447B LEU* 3.6 27.8 - - + -
450B LEU* 3.6 23.8 - - + -
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Residues in contact with ALA 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B LEU 2.9 4.9 + - - -
390B TYR 2.8 15.3 + - - +
392B LEU* 1.3 75.2 - - - +
394B GLN* 1.3 51.7 + - - +
395B TYR 2.6 13.9 + - - -
396B ALA* 2.8 23.0 + - - +
402B GLN* 3.6 30.8 - - - +
405B LEU* 3.8 24.4 - - + +
406B ARG* 3.9 20.0 - - + +
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Residues in contact with GLN 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B SER* 3.6 35.1 + - - -
390B TYR 4.1 2.0 + - - +
391B GLU* 3.1 22.9 - - - +
392B LEU 3.1 0.2 + - - -
393B ALA* 1.3 75.8 - - - +
395B TYR* 1.3 101.3 + - + +
396B ALA 3.4 1.7 + - - -
402B GLN* 4.2 7.7 - - - +
406B ARG* 4.3 15.7 - - - +
446B HIS* 4.7 3.9 + - - -
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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