Contacts of the strand formed by residues 353 - 358 (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 CYS 353 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2062 ASN 4.6 0.2 - - - -
2072 ASN 3.9 12.1 - - - -
2082 GLU* 3.2 35.9 - - - -
2092 ILE 3.4 5.3 - - - +
2102 GLY* 3.3 22.3 - - - +
2352 GLN* 5.5 0.7 - - + -
2582 LYS* 4.0 8.3 - - - +
3492 HIS* 4.7 0.2 + - - -
3502 TYR* 2.8 31.5 - - + +
3522 GLY* 1.4 78.1 - - - +
3542 ILE* 1.4 62.2 + - - +
4072 ARG* 3.6 25.6 - - - +
4082 PHE 4.5 0.4 - - - -
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Residues in contact with ILE 354 (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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2092 ILE 3.5 3.8 - - - -
3302 ILE* 3.8 15.7 - - + -
3422 MET* 3.7 28.5 - - + -
3432 ASN 4.2 2.7 - - - +
3492 HIS* 3.7 29.6 - - + +
3512 PRO 3.7 15.9 - - - +
3532 CYS* 1.4 80.1 - - - +
3552 ASN* 1.3 69.0 + - - +
3562 LEU* 4.2 9.4 - - + -
4072 ARG* 3.1 7.3 - - - +
4082 PHE* 2.9 47.7 + - + +
4102 ILE* 3.9 17.9 - - + -
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Residues in contact with ASN 355 (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* 3.5 24.1 + - - +
2092 ILE* 3.3 34.3 + - + +
3432 ASN* 3.1 32.0 + - + +
3542 ILE* 1.3 75.3 - - - +
3562 LEU* 1.3 67.1 + - - +
3572 SER* 3.7 13.5 + - - -
3782 GLY* 3.4 28.9 + - - -
3912 VAL 5.2 0.2 - - - +
3922 LEU* 3.6 21.6 - - - +
4062 ILE 3.5 13.6 + - - -
4072 ARG* 4.6 2.4 - - - +
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Residues in contact with LEU 356 (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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3342 MET* 5.3 1.3 - - + -
3402 VAL* 4.3 15.3 - - + -
3412 VAL 3.5 19.3 - - - +
3422 MET* 3.8 13.9 - - + -
3542 ILE* 3.9 12.5 + - + -
3552 ASN* 1.3 81.5 - - - +
3572 SER* 1.4 60.1 + - - +
3582 PHE* 3.4 36.2 - - + -
3702 LEU* 3.5 31.6 - - + -
4052 SER* 3.8 4.2 - - - -
4062 ILE* 3.1 28.5 + - + +
4082 PHE* 4.3 20.4 - - + +
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Residues in contact with SER 357 (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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3412 VAL* 3.6 4.7 + - - -
3432 ASN* 3.3 23.3 + - - -
3552 ASN* 3.7 9.5 + - - -
3562 LEU* 1.4 71.7 - - - +
3582 PHE* 1.4 72.6 + - - +
3922 LEU* 3.0 33.8 + - - +
3952 ILE* 3.5 10.8 + - - -
3972 THR* 3.3 17.3 - - - +
4012 LEU 4.2 3.1 - - - +
4052 SER* 3.3 17.5 + - - -
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Residues in contact with PHE 358 (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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3392 ASP 3.6 17.3 - - - +
3402 VAL* 3.9 25.4 - - + -
3412 VAL* 3.7 27.4 + - - +
3562 LEU* 3.4 38.6 - - + -
3572 SER* 1.4 90.8 - - - +
3592 ALA* 1.4 67.0 + - - +
3612 VAL* 4.0 4.9 - - + -
3662 LEU* 3.5 53.8 - - + -
3692 ALA* 5.3 8.1 - - + -
3702 LEU* 5.5 0.7 - - + -
3952 ILE* 4.5 1.9 - - - +
3962 GLY 3.8 2.8 - - - +
3972 THR* 3.4 11.0 - - - +
4012 LEU* 4.4 1.8 - - + -
4042 SER 4.3 7.0 - - - -
4052 SER* 4.5 1.1 - - - -
4062 ILE* 4.2 19.7 - - + -
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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