Contacts of the helix formed by residues 356 - 366 (chain 1) in PDB entry 6Q8W
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 CYS 356 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3531 CYS* 5.2 2.1 - - - -
3541 GLY 4.6 0.2 - - - -
3551 LYS* 1.3 77.8 + - - +
3571 THR* 1.3 58.6 + - - +
3581 PRO* 3.6 20.0 - - + -
3591 CYS* 4.5 12.1 - - + +
3601 ARG* 2.6 36.1 + - - +
3981 SER* 5.4 2.0 - - - -
3991 PHE* 3.5 39.7 - - - -
4001 CYS* 5.2 2.5 - - - -
433 GLY 4.1 10.1 - - - -
443 ALA 3.2 8.5 - - - +
463 ARG* 4.6 3.1 - - - -
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Residues in contact with THR 357 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3551 LYS 3.6 0.8 + - - -
3561 CYS* 1.3 70.1 - - - +
3581 PRO* 1.4 71.2 - - - +
3601 ARG* 3.1 27.8 + - - +
3611 GLU* 2.9 38.9 + - + +
443 ALA 3.1 9.0 + - - -
453 CYS* 3.9 16.5 - - - +
1073 MET* 5.4 2.0 - - + +
1103 PHE* 4.5 2.9 - - + +
1113 THR* 3.6 32.3 - - + +
1823 ILE* 3.6 14.2 + - + +
1833 HIS 3.8 7.3 + - - -
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Residues in contact with PRO 358 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3561 CYS* 3.5 12.3 - - + -
3571 THR* 1.4 91.8 - - - +
3591 CYS* 1.3 60.4 + - - +
3621 GLY* 2.9 30.3 + - - -
3631 VAL 3.9 0.5 + - - -
3931 LEU 5.0 5.2 - - - +
3941 ILE* 4.8 9.0 - - - +
3971 ARG 4.5 9.2 - - - +
3981 SER* 4.6 6.1 - - - +
443 ALA 3.6 7.4 - - - +
453 CYS 4.4 0.4 - - - +
463 ARG* 3.7 27.6 - - + -
1073 MET* 3.3 33.2 - - + -
1103 PHE* 4.6 11.9 - - + -
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Residues in contact with CYS 359 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3481 TYR 5.9 1.1 - - - -
3521 SER* 4.0 22.8 - - - -
3531 CYS 5.6 0.7 - - - -
3561 CYS* 4.2 12.5 + - + -
3571 THR 3.5 0.4 - - - -
3581 PRO* 1.3 80.0 - - - +
3601 ARG* 1.3 68.2 + - - +
3631 VAL* 2.9 39.8 + - - +
3641 ALA 3.9 0.2 + - - -
3941 ILE* 4.6 5.5 - - - +
3981 SER* 4.7 3.8 - - - +
4001 CYS* 6.3 2.0 - - - -
4021 LEU* 4.9 11.4 - - - -
4031 ALA* 4.0 31.0 - - + -
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Residues in contact with ARG 360 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3521 SER* 3.7 20.9 - - - +
3541 GLY* 3.8 20.6 + - - -
3551 LYS 3.9 1.0 + - - -
3561 CYS 2.6 42.7 + - - +
3571 THR* 3.1 32.8 + - - +
3591 CYS* 1.3 83.9 - - - +
3611 GLU* 1.3 81.4 + - - +
3641 ALA* 3.0 21.4 + - - +
1823 ILE 3.2 16.8 + - - -
1833 HIS* 3.4 27.5 + - - +
2063 GLY 3.2 30.5 - - - +
2073 VAL* 3.1 23.8 - - + +
2093 THR* 4.5 0.2 - - - -
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Residues in contact with GLU 361 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3571 THR* 2.9 22.1 + - + +
3601 ARG* 1.3 106.3 + - - +
3621 GLY* 1.3 67.7 + - - +
3651 GLY* 2.8 20.3 + - - -
3661 PHE 3.1 5.5 + - - -
1103 PHE* 3.4 26.7 - - + +
1113 THR* 5.3 2.9 - - - +
1133 LEU* 3.4 14.2 - - + +
1143 ASN* 3.3 16.4 + - - -
1623 ARG* 2.3 36.1 + - - -
1833 HIS* 3.6 2.9 - - - -
2073 VAL* 4.1 5.1 - - - +
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Residues in contact with GLY 362 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3581 PRO 2.9 20.5 + - - -
3611 GLU* 1.3 73.0 - - - +
3631 VAL* 1.3 55.7 + - - -
3661 PHE* 2.8 27.1 + - - +
3671 MET* 2.8 15.3 + - - -
3941 ILE* 4.5 2.7 - - - -
1103 PHE* 3.8 33.4 - - - -
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Residues in contact with VAL 363 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3451 THR* 4.3 9.4 - - - +
3481 TYR 4.6 2.0 - - - +
3491 ALA* 4.3 21.3 - - - +
3591 CYS* 2.9 32.6 + - + +
3621 GLY* 1.3 74.8 - - - +
3641 ALA* 1.3 61.0 + - + +
3671 MET* 3.2 17.4 + - + -
3681 VAL* 3.0 27.2 + - - +
3941 ILE* 3.9 30.1 - - + -
4031 ALA* 5.2 1.6 - - + -
4061 ALA* 4.1 27.4 - - + -
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Residues in contact with ALA 364 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3491 ALA* 3.5 38.1 - - + +
3521 SER* 5.3 2.5 - - - -
3601 ARG* 3.0 18.2 + - - +
3631 VAL* 1.3 78.5 - - - +
3651 GLY* 1.3 56.7 + - - +
3681 VAL* 3.2 14.1 - - - +
3691 ASN* 4.7 1.9 + - - -
2073 VAL* 3.6 31.1 - - + +
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Residues in contact with GLY 365 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3601 ARG 3.8 1.4 + - - -
3611 GLU 2.8 13.3 + - - -
3641 ALA* 1.3 79.9 - - - +
3661 PHE* 1.3 59.1 + - - +
3681 VAL* 4.7 0.2 - - - -
3691 ASN* 2.3 38.9 + - - +
1133 LEU* 4.1 9.2 - - - -
1143 ASN* 5.1 5.2 - - - -
1573 PHE* 3.5 10.3 - - - -
2073 VAL* 4.0 7.1 - - - +
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Residues in contact with PHE 366 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3611 GLU 3.1 2.0 + - - +
3621 GLY* 2.8 24.6 + - - +
3651 GLY* 1.3 71.4 - - - +
3671 MET* 1.3 53.5 + - + +
3681 VAL 3.4 0.2 - - - -
3691 ASN* 2.8 8.0 + - - +
3701 LEU* 2.8 57.6 + - + +
3861 ASN* 5.6 4.3 - - + -
3901 LEU* 3.5 39.0 - - + -
1093 GLU* 3.8 19.3 - - - -
1103 PHE* 3.7 12.1 - + + -
1133 LEU* 4.3 10.3 - - + +
1563 ARG* 3.8 28.7 - - + -
1573 PHE* 3.9 31.2 - + + -
1593 PHE* 4.1 6.5 - + - -
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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