Contacts of the strand formed by residues 405 - 409 (chain 2) 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 SER 405 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3562 LEU 3.8 11.7 - - - -
3572 SER* 3.3 15.4 + - - -
3582 PHE* 4.5 3.6 - - - -
3672 LEU* 5.2 0.2 - - - +
3772 SER 4.0 7.6 - - - +
3782 GLY 3.7 11.2 - - - +
3792 SER 3.6 17.5 - - - +
3802 ALA* 5.3 0.9 - - - +
3922 LEU* 3.7 20.8 - - - +
3972 THR* 4.8 0.2 - - - +
4012 LEU 3.1 15.5 + - - -
4022 ALA* 3.3 13.0 + - - -
4032 HIS 4.5 3.3 - - - +
4042 SER* 1.4 80.5 - - - +
4062 ILE* 1.4 61.7 + - - +
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Residues in contact with ILE 406 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3552 ASN* 3.5 6.9 + - - -
3562 LEU* 3.1 30.0 + - + +
3582 PHE* 4.2 17.4 - - + -
3662 LEU 4.0 17.3 - - - +
3672 LEU* 3.6 35.2 - - + +
3702 LEU* 4.2 34.5 - - + +
3762 SER 5.8 0.2 - - - -
3772 SER 4.7 2.7 - - - +
3782 GLY* 4.2 8.3 - - - -
4042 SER 3.6 2.4 + - - +
4052 SER* 1.4 75.0 - - - +
4072 ARG* 1.4 65.8 + - - +
4082 PHE* 5.9 0.2 - - - -
103j SER* 5.4 3.8 - - - +
107j GLU* 6.2 1.1 - - - +
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Residues in contact with ARG 407 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2082 GLU* 4.5 5.6 - - - +
2582 LYS* 3.4 24.6 - - - +
3522 GLY 3.1 21.2 + - - -
3532 CYS* 3.6 24.8 - - - +
3542 ILE 3.1 22.7 - - - +
3552 ASN* 4.5 3.1 - - - +
3732 VAL* 4.2 5.9 - - - +
3742 ALA* 3.2 55.1 + - - +
3752 LEU 3.4 9.9 + - - -
3762 SER* 3.3 42.3 + - - +
3782 GLY* 4.3 11.7 - - - -
4062 ILE* 1.4 83.3 - - - +
4082 PHE* 1.4 70.1 + - - +
4092 GLY 3.9 0.7 + - - -
107j GLU* 4.6 2.9 - - - +
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Residues in contact with PHE 408 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3292 LEU* 3.8 25.8 - - + -
3302 ILE* 4.8 7.2 - - + -
3332 ILE* 4.3 13.9 - - + -
3532 CYS* 4.4 1.4 - - - -
3542 ILE* 2.9 45.1 + - + +
3562 LEU* 4.3 21.5 - - + +
3702 LEU* 3.7 36.8 - - + -
3732 VAL* 3.9 24.2 - - + -
4062 ILE* 4.3 0.8 - - - -
4072 ARG* 1.4 84.9 + - - +
4092 GLY* 1.4 70.8 + - - +
4102 ILE* 3.8 21.8 + - + -
4222 THR* 5.0 6.3 - - + -
4252 LYS* 4.7 4.9 - - - -
4262 CYS* 4.9 2.2 - - - -
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Residues in contact with GLY 409 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3522 GLY 4.8 4.0 - - - -
3732 VAL* 3.3 40.1 - - - +
3742 ALA* 3.9 22.0 + - - -
4072 ARG* 4.9 0.4 - - - -
4082 PHE* 1.4 74.5 - - - +
4102 ILE* 1.4 72.3 + - - +
4112 GLY 3.9 1.5 + - - -
4132 PHE* 5.2 5.0 - - - -
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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