Contacts of the helix formed by residues 606 - 610 (chain 3) 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 THR 606 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3003 TRP* 3.4 36.6 - - + -
3013 ALA* 4.8 2.0 - - + +
3053 ARG* 3.2 20.3 + - - +
5883 SER* 4.1 15.3 - - - +
5893 HIS* 5.5 0.7 - - + -
6053 PRO* 1.3 79.9 - - - +
6073 PHE* 1.3 68.5 + - - +
6083 TYR* 3.0 17.6 - - - +
6093 GLU* 3.1 29.2 + - - +
6103 LYS* 3.2 12.5 + - - +
6293 ILE* 5.4 0.2 - - - +
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Residues in contact with PHE 607 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2543 THR* 4.4 2.2 + - + -
2553 THR 3.6 17.9 - - - -
2563 CYS* 3.6 18.6 - - + -
2573 ALA* 3.6 38.1 - - + -
2583 LEU* 4.6 17.5 - - + -
2653 ILE* 4.3 1.3 - - + -
3003 TRP* 4.4 15.5 - + - -
3483 ASP* 5.2 13.6 + - + -
6063 THR* 1.3 74.6 - - - +
6083 TYR* 1.3 111.2 + + - +
6093 GLU 3.2 0.7 + - - -
6103 LYS* 3.4 24.8 + - - +
6243 LEU* 3.3 32.3 - - + +
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Residues in contact with TYR 608 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2543 THR* 4.9 7.4 - - + +
2563 CYS* 5.6 1.0 - - - -
2583 LEU* 5.3 2.4 - - - +
2653 ILE* 3.8 20.3 - - + +
2673 ALA* 4.6 8.1 - - + -
2743 LEU* 3.7 24.5 - - + -
2773 ILE* 3.9 26.3 - - + +
2943 GLY 3.7 19.2 + - - -
2973 GLY 4.5 3.8 + - - -
2983 HIS* 4.0 11.3 - - + +
3003 TRP* 4.6 8.7 - + - -
3013 ALA* 4.2 16.2 - - + -
6063 THR* 3.0 10.5 - - - +
6073 PHE* 1.3 120.1 - + - +
6093 GLU* 1.3 57.4 + - - +
6253 SER 3.8 5.4 - - - +
6273 ALA* 3.1 29.2 + - + +
6293 ILE* 3.8 17.9 - - + -
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Residues in contact with GLU 609 (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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3053 ARG* 2.3 49.7 + - - -
6053 PRO* 3.2 15.5 - - + +
6063 THR* 3.1 20.8 + - - +
6083 TYR* 1.3 75.9 - - - +
6103 LYS* 1.3 59.8 + - - +
6263 PRO* 3.7 12.9 - - - +
6273 ALA 3.7 20.6 - - - +
6293 ILE* 3.8 22.7 - - + +
6313 ASN* 3.1 31.5 - - + +
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Residues in contact with LYS 610 (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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3483 ASP* 3.6 34.1 + - - -
3503 THR* 4.4 13.1 - - + +
3533 GLU* 3.9 27.1 + - - +
6053 PRO* 3.8 34.7 + - + +
6063 THR 3.2 14.1 + - - +
6073 PHE* 3.4 21.0 + - - +
6093 GLU* 1.3 80.0 - - - +
6113 ARG* 1.3 62.0 + - - +
6243 LEU* 3.7 11.9 - - + +
6253 SER 2.8 28.9 - - - +
6263 PRO* 3.0 2.7 - - - -
6363 GLY* 5.9 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
------------------------------------------------------------
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