Contacts of the helix formed by residues 540 - 547 (chain 3) in PDB entry 6Q8O
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 ASN 540 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3473 HIS 3.2 19.4 + - - +
3483 ASP 4.5 1.1 - - - -
3493 ALA 2.3 35.8 + - - +
3503 THR* 3.5 15.6 - - - +
3513 LEU* 3.7 8.8 - - - +
5393 ALA* 1.3 75.6 - - - +
5413 ALA* 1.3 64.6 + - - +
5423 ARG 3.5 2.0 - - - -
5433 GLY 3.3 0.6 + - - -
5443 LEU* 3.2 17.5 + - + +
6143 LEU* 3.2 28.4 - - + +
6153 VAL* 2.6 37.2 + - - +
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Residues in contact with ALA 541 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3713 PHE* 4.2 13.2 - - + -
3733 GLY 5.2 1.1 - - - +
3753 THR* 6.3 1.1 - - + -
3793 ALA* 5.8 0.2 - - + -
5363 THR* 4.1 17.0 - - + +
5383 ALA* 3.7 31.1 - - + +
5393 ALA 3.2 4.2 + - - -
5403 ASN* 1.3 76.5 - - - +
5423 ARG* 1.3 60.8 + - - +
5443 LEU* 2.7 32.8 + - - +
5453 GLU* 2.9 20.6 + - - +
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Residues in contact with ARG 542 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3793 ALA* 2.8 35.5 + - + +
3803 SER* 3.4 24.4 + - - +
3823 PHE* 3.5 22.3 + - - +
3833 PRO 5.9 0.2 + - - -
3843 PRO* 4.9 13.2 - - - +
5323 VAL 5.4 2.2 + - - -
5343 ALA* 3.3 27.7 + - - +
5363 THR* 5.2 4.7 - - + +
5393 ALA 5.0 0.4 + - - -
5403 ASN 3.5 0.2 - - - -
5413 ALA* 1.3 78.3 - - - +
5433 GLY* 1.3 56.6 + - - +
5453 GLU* 3.9 10.7 - - - +
5463 ALA* 2.9 29.5 + - - +
6153 VAL* 4.2 8.6 + - + -
6163 ASN 4.1 19.7 - - - +
6173 LEU* 3.3 27.9 + - - +
6183 GLU 5.2 0.2 - - - -
6193 GLY* 4.4 11.0 - - - +
6763 LEU* 5.3 9.2 - - + -
6783 PHE* 5.0 6.2 + - + +
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Residues in contact with GLY 543 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3513 LEU* 3.4 26.9 - - - -
5403 ASN 3.3 5.4 + - - -
5413 ALA 3.0 1.0 - - - -
5423 ARG* 1.3 77.0 - - - +
5443 LEU* 1.3 54.0 + - - +
5463 ALA* 3.2 3.7 + - - +
5473 MET* 2.7 39.8 + - - +
6153 VAL* 3.5 20.6 - - - +
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Residues in contact with LEU 544 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3453 LEU* 4.4 7.9 - - + -
3463 ALA 3.9 14.8 - - - +
3473 HIS* 4.6 6.1 - - - +
3493 ALA* 3.6 31.4 - - + +
3503 THR 4.2 1.8 - - - +
3513 LEU* 4.5 0.6 - - - +
3543 GLY* 3.8 23.1 - - - -
3713 PHE* 3.7 39.9 - - + -
5403 ASN 3.2 16.2 + - - +
5413 ALA* 2.7 14.4 + - - +
5433 GLY* 1.3 70.6 - - - +
5453 GLU* 1.3 57.3 + - - +
5473 MET* 3.1 7.5 + - - -
5483 GLY 2.9 22.3 + - - -
5493 VAL* 3.0 22.2 + - + +
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Residues in contact with GLU 545 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3713 PHE* 4.1 18.0 - - + -
3753 THR* 4.0 6.9 + - - +
3783 PRO* 3.8 10.6 - - + +
3793 ALA* 3.2 25.1 + - - +
3803 SER* 2.3 49.7 + - - +
5413 ALA* 2.9 22.0 + - - +
5423 ARG* 3.9 8.0 - - - +
5443 LEU* 1.3 75.0 - - - +
5463 ALA* 1.3 55.3 + - - +
5483 GLY* 2.6 25.5 + - - -
5503 LEU* 3.9 32.4 - - + +
6783 PHE* 3.7 12.4 - - + -
6803 LEU* 5.1 2.2 - - + +
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Residues in contact with ALA 546 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5423 ARG 2.9 20.5 + - - +
5433 GLY* 3.2 7.8 + - - +
5453 GLU* 1.3 74.9 - - - +
5473 MET* 1.3 73.9 + - + +
5483 GLY 3.3 0.6 + - - -
6153 VAL* 5.6 0.9 - - + -
6673 ARG* 4.0 13.3 + - - -
6763 LEU* 3.8 29.6 - - + -
6783 PHE* 3.6 28.8 - - + -
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Residues in contact with MET 547 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3513 LEU* 3.6 36.8 - - + +
3543 GLY 4.1 3.4 - - - -
3553 LEU* 3.6 39.4 - - - +
3583 SER* 3.3 19.2 + - - -
5433 GLY 2.7 22.0 + - - +
5443 LEU* 3.3 7.2 - - - +
5453 GLU 3.0 0.2 - - - -
5463 ALA* 1.3 96.1 - - + +
5483 GLY* 1.3 60.9 + - - +
5493 VAL* 3.7 0.4 - - - -
6643 LEU* 3.5 33.2 - - + -
6673 ARG* 4.7 20.3 + - + +
6693 VAL* 4.4 13.7 - - + -
6763 LEU* 6.3 0.9 - - + -
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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