Contacts of the strand formed by residues 396 - 399 (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 ALA 396 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3903 LEU* 4.6 4.9 - - + -
3953 PHE* 1.3 81.3 - - - +
3973 LEU* 1.3 60.8 + - - +
3983 VAL* 3.5 17.2 + - + +
4133 LEU* 4.5 5.6 - - + -
4163 PHE* 3.8 20.9 - - + -
4473 LYS 3.3 4.6 + - - -
4483 MET* 3.5 4.6 - - + -
4493 ALA 3.0 29.3 + - - +
5043 VAL 3.4 4.9 - - - -
5063 ILE* 4.3 15.5 - - + -
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Residues in contact with LEU 397 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3953 PHE* 4.1 8.6 - - + -
3963 ALA* 1.3 69.4 - - - +
3983 VAL* 1.3 62.5 + - - +
3993 LEU* 3.9 10.0 - - + +
4493 ALA* 3.6 9.4 - - + +
4513 PHE* 4.2 21.1 - - + -
4763 ILE* 5.7 0.2 - - + -
4803 LEU* 3.4 35.7 - - + -
4933 ALA* 4.3 15.9 - - + -
4973 TRP* 3.9 34.1 - - + -
5043 VAL 3.0 9.6 + - - +
5053 LEU* 3.6 23.0 - - + +
5063 ILE 2.9 25.7 + - - +
5243 LEU* 4.3 1.6 - - + -
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Residues in contact with VAL 398 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3963 ALA* 3.6 28.7 - - + +
3973 LEU* 1.3 74.7 - - - +
3993 LEU* 1.3 67.3 + - - +
4003 GLY 3.6 19.7 - - - +
4023 PRO* 3.9 19.1 - - + -
4133 LEU* 5.1 3.4 - - + -
4483 MET* 4.3 16.6 - - + -
4493 ALA 2.9 11.2 + - - +
4503 LEU* 3.5 10.0 - - + -
4513 PHE* 2.9 26.0 + - - +
5063 ILE* 3.4 32.8 - - + -
5353 MET* 4.4 0.7 - - + -
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Residues in contact with LEU 399 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3973 LEU* 3.9 23.1 - - + +
3983 VAL* 1.3 80.8 - - - +
4003 GLY* 1.3 54.2 + - - +
4513 PHE* 3.3 15.7 - - + +
4733 GLU* 3.6 23.6 - - + -
4763 ILE* 4.7 12.3 - - + -
4773 LEU* 3.6 31.4 - - + -
4803 LEU* 5.6 0.4 - - + -
5053 LEU* 3.9 18.6 - - + -
5063 ILE 2.9 12.8 + - - +
5073 LEU* 3.4 8.5 - - + -
5083 GLY* 2.5 35.7 + - - -
5113 VAL* 3.8 19.0 - - + +
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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