Contacts of the helix formed by residues 406 - 418 (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 ALA 406 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2603 PRO* 5.9 0.2 - - + -
2613 VAL* 3.9 17.7 - - + -
4023 PRO* 2.9 13.0 + - - +
4053 GLU* 1.3 78.5 - - - +
4073 PRO* 1.3 68.9 - - - +
4083 ILE 3.5 1.6 - - - -
4093 LEU* 3.1 32.7 + - + +
5353 MET* 3.6 32.1 - - + -
6173 LEU* 4.7 4.3 - - + -
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Residues in contact with PRO 407 (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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2223 PHE* 3.3 27.4 - - + -
2593 CYS* 3.5 28.5 - - + -
2613 VAL* 4.6 2.7 - - + -
2913 CYS* 4.0 23.6 - - + -
4023 PRO 3.4 7.6 - - - +
4033 THR 4.1 7.4 - - - +
4043 GLU 4.0 11.7 - - - +
4053 GLU 3.6 3.1 - - - +
4063 ALA* 1.3 86.3 - - - +
4083 ILE* 1.3 60.4 + - + +
4103 HIS* 2.9 32.2 + - - +
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Residues in contact with ILE 408 (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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2223 PHE* 4.7 2.2 - - + -
2613 VAL* 3.8 25.8 - - + -
2633 CYS* 3.4 28.7 - - - -
2853 VAL* 3.5 33.2 - - + +
2863 ASN* 4.1 10.5 - - + -
2893 TRP* 5.1 5.8 - - + +
2903 ILE 5.5 0.2 - - - -
2913 CYS* 5.2 9.0 - - + +
3873 LEU* 3.6 20.9 - - + -
4073 PRO* 1.3 74.4 - - + +
4093 LEU* 1.3 70.6 + - + +
4103 HIS 3.1 0.2 - - - -
4113 LEU* 2.9 25.5 + - + +
4123 ARG* 2.9 26.4 + - + +
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Residues in contact with LEU 409 (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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2613 VAL* 5.3 2.5 - - + -
3873 LEU* 3.5 38.4 - - + -
3903 LEU* 4.5 12.1 - - + -
4023 PRO* 4.5 7.2 - - + -
4063 ALA* 3.1 32.7 + - + +
4073 PRO 3.1 0.6 + - - -
4083 ILE* 1.3 82.1 - - + +
4103 HIS* 1.3 51.8 + - - +
4123 ARG* 3.0 5.6 + - + +
4133 LEU* 2.4 46.0 + - + +
5063 ILE* 4.3 15.9 - - + -
5333 LEU* 3.7 22.7 - - + -
5353 MET* 4.0 14.6 - - + -
6173 LEU* 5.3 4.3 - - + -
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Residues in contact with HIS 410 (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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1943 VAL 3.8 2.9 - - - -
1953 PRO* 2.3 45.0 + - + +
1973 ASP* 5.2 5.6 - - - -
2223 PHE* 3.9 20.7 - + + -
4023 PRO* 4.6 2.1 - - - +
4033 THR* 3.3 32.8 + - + +
4063 ALA 3.9 1.0 + - - -
4073 PRO 2.9 16.8 + - - +
4093 LEU* 1.3 76.0 - - - +
4113 LEU* 1.3 59.3 + - + +
4133 LEU* 3.0 16.7 + - - +
4143 SER* 2.9 23.6 + - - -
4573 PRO* 5.7 6.1 - - + -
4583 LEU* 3.9 18.3 - - + +
4613 TRP* 3.5 13.6 - + - -
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Residues in contact with LEU 411 (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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1903 TYR* 5.0 2.0 - - + -
1943 VAL* 3.4 31.5 - - + +
1953 PRO* 4.0 13.9 - - + -
2223 PHE* 4.0 37.2 - - + -
2253 ASN* 4.4 8.1 - - - +
2873 GLU* 5.8 0.7 - - - +
2893 TRP* 3.5 46.2 - - + -
4083 ILE* 2.9 21.7 + - + +
4103 HIS* 1.3 76.6 - - + +
4123 ARG* 1.3 67.1 + - - +
4143 SER* 2.9 19.9 + - - -
4153 GLU* 3.1 9.5 + - - +
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Residues in contact with ARG 412 (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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2833 PRO 2.7 29.9 + - - -
2843 GLU 3.4 7.2 + - - -
2853 VAL 2.7 34.5 + - - +
2863 ASN* 4.4 2.4 - - - +
2873 GLU* 4.0 23.0 + - - +
2893 TRP* 5.5 1.6 - - - -
3873 LEU* 4.5 15.2 - - + +
3883 GLU* 4.7 9.3 + - - +
3903 LEU* 4.5 13.9 - - + -
3913 LEU* 3.3 23.8 - - + +
4083 ILE* 2.9 27.5 + - + +
4093 LEU* 3.5 9.4 - - + +
4113 LEU* 1.3 79.1 - - - +
4133 LEU* 1.3 58.0 + - - +
4153 GLU* 2.9 35.1 + - - +
4163 PHE* 2.8 24.1 + - - +
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Residues in contact with LEU 413 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3903 LEU* 4.3 16.2 - - + -
3963 ALA* 4.6 11.9 - - + -
3983 VAL* 5.4 1.8 - - + -
4023 PRO* 4.3 17.0 - - + -
4093 LEU* 2.4 34.8 + - + +
4103 HIS* 3.1 10.8 - - - +
4123 ARG* 1.3 73.0 - - - +
4143 SER* 1.3 51.5 + - - +
4163 PHE* 2.9 24.8 + - + +
4173 VAL* 2.6 39.3 + - - +
4483 MET* 4.4 21.8 - - + -
4583 LEU* 4.0 21.8 - - + -
4613 TRP* 4.8 8.5 - - + -
5063 ILE* 4.9 10.5 - - + -
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Residues in contact with SER 414 (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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1933 GLU 2.7 6.8 + - - -
1943 VAL* 3.0 25.4 + - - -
4103 HIS 2.9 8.3 + - - -
4113 LEU 2.9 11.6 + - - -
4133 LEU* 1.3 75.9 - - - +
4153 GLU* 1.3 55.5 + - - +
4173 VAL* 4.0 5.4 - - - -
4183 ARG* 2.2 46.7 + - - +
4433 ARG* 2.2 34.5 + - - +
4613 TRP* 4.4 6.0 - - - -
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Residues in contact with GLU 415 (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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383 HIS* 3.8 13.4 + - - +
1943 VAL* 6.3 0.7 - - + -
2873 GLU* 2.7 27.1 - - - +
3913 LEU* 3.2 19.1 - - + +
4113 LEU 3.1 10.9 + - - +
4123 ARG* 2.9 41.2 + - - +
4143 SER* 1.3 77.9 - - - +
4163 PHE* 1.3 59.8 + - - +
4183 ARG* 3.1 18.7 + - - +
4203 LEU* 2.9 52.0 + - + +
4213 LYS 5.5 1.4 - - - +
4233 PRO* 6.0 2.2 - - - +
4373 ILE* 5.6 1.4 - - - +
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Residues in contact with PHE 416 (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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3903 LEU* 3.7 23.3 - - + +
3913 LEU* 3.4 21.3 - - + +
3933 ALA* 3.4 24.0 - - + -
3943 ASP 3.9 9.9 - - - -
3953 PHE* 4.4 4.0 - - - -
3963 ALA* 3.8 16.2 - - + -
4123 ARG 2.8 16.7 + - - +
4133 LEU* 2.9 25.8 + - + +
4153 GLU* 1.3 74.3 - - - +
4173 VAL* 1.3 67.3 + - + +
4193 ASP* 3.0 15.8 + - - -
4203 LEU 4.9 2.9 - - - +
4473 LYS* 3.0 66.6 + - + +
4483 MET* 4.3 3.8 - - + -
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Residues in contact with VAL 417 (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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4133 LEU 2.6 21.7 + - - +
4143 SER* 3.7 11.0 - - - +
4163 PHE* 1.3 76.9 - - + +
4183 ARG* 1.3 60.0 + - - +
4193 ASP 3.3 1.6 + - - -
4433 ARG* 3.7 32.3 - - + +
4443 ARG* 3.1 62.8 + - + +
4473 LYS* 4.8 8.7 - - + -
4483 MET* 4.3 26.7 - - + -
4613 TRP* 4.3 11.2 - - + -
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Residues in contact with ARG 418 (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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383 HIS 5.1 5.9 + - - -
1933 GLU* 3.7 32.4 + - - +
1943 VAL* 4.5 11.7 - - - +
4113 LEU 4.4 0.4 + - - -
4143 SER* 2.2 55.4 + - - +
4153 GLU* 3.1 20.7 + - - +
4163 PHE 3.1 1.6 + - - -
4173 VAL* 1.3 81.7 - - + +
4193 ASP* 1.3 66.4 + - - +
4203 LEU* 3.1 21.8 - - + +
4373 ILE* 4.8 3.2 - - - +
4413 MET* 3.2 56.7 - - + +
4423 PRO 4.1 14.0 - - - +
4433 ARG* 3.3 22.2 - - + +
4443 ARG* 5.8 0.7 - - - -
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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