Contacts of the helix formed by residues 399 - 403 (chain 3) in PDB entry 5KZ5
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 GLU 399 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3793 SER* 2.9 46.1 + - - +
3803 ALA* 3.9 16.4 - - + -
3813 CYS* 3.5 26.5 + - - +
3933 ARG* 3.7 14.9 - - - +
3983 ASP* 1.3 81.2 - - - +
4003 ASP* 1.4 64.9 + - - +
4033 HIS* 3.4 14.5 + - - +
71f ASP* 5.1 2.0 - - - +
94f GLY* 3.4 28.2 - - - +
95f CYS* 3.4 19.3 - - - -
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Residues in contact with ASP 400 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3983 ASP* 3.0 23.9 - - - +
3993 GLU* 1.4 84.3 + - - +
4013 LEU* 1.4 76.8 + - - +
4033 HIS* 3.3 7.0 + - - +
4043 SER* 2.9 31.5 + - - -
364O GLU* 5.5 2.2 - - - +
398O ASP* 5.5 0.9 - - - +
399O GLU* 3.2 27.7 - - - +
400O ASP* 4.4 11.2 - - - +
94f GLY 4.9 3.5 + - - +
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Residues in contact with LEU 401 (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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3573 SER* 3.0 26.1 + - - +
3583 PHE 3.9 9.4 - - - +
3593 ALA* 3.5 34.1 - - + -
3603 TYR 4.8 2.5 - - - +
3613 VAL* 5.6 5.2 - - + +
3633 GLY* 5.3 13.7 - - - -
3673 LEU* 5.5 6.2 - - + +
3973 THR* 4.1 4.0 - - - -
3983 ASP* 3.3 31.3 + - + +
4003 ASP* 1.4 91.3 - - - +
4023 ALA* 1.4 60.7 + - - +
4043 SER* 3.3 10.9 + - - +
4053 SER* 3.2 15.8 + - - -
399O GLU* 6.2 0.4 - - + -
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Residues in contact with ALA 402 (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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3573 SER* 4.8 0.4 - - - -
3763 SER 4.0 0.2 - - - +
3773 SER 3.3 14.2 - - - +
3793 SER* 3.5 20.6 - - - +
3923 LEU* 3.4 19.9 - - + +
3933 ARG* 4.2 7.2 - - - -
3973 THR* 3.5 22.1 + - - +
3983 ASP 3.0 13.5 + - - +
4013 LEU* 1.4 75.6 - - - +
4033 HIS* 1.4 59.2 + - - +
4053 SER* 2.9 23.4 + - - -
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Residues in contact with HIS 403 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3753 LEU* 3.4 35.6 - - + +
3763 SER 3.1 15.5 - - - +
3773 SER* 3.2 33.4 + - - -
3793 SER* 3.9 7.6 - - - -
3813 CYS* 3.4 36.3 + - + +
3993 GLU* 3.4 17.4 + - - +
4003 ASP* 3.3 7.7 + - - +
4023 ALA* 1.4 77.6 - - - +
4043 SER* 1.4 56.0 + - - +
4053 SER 3.4 1.1 - - - -
457O HIS* 4.1 23.7 - + - -
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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