Contacts of the strand formed by residues 353 - 358 (chain 1) 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 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2061 ASN 5.4 0.2 - - - +
2071 ASN 4.5 3.6 - - - +
2081 GLU 3.2 28.5 - - - -
2091 ILE 3.7 8.3 - - - -
2101 GLY* 3.4 21.1 - - - +
2351 GLN* 6.5 0.9 - - + -
3491 HIS* 5.1 0.7 + - - -
3501 TYR* 2.9 29.9 + - + +
3511 PRO 3.2 0.4 - - - -
3521 GLY* 1.4 76.9 - - - +
3541 ILE* 1.3 71.5 + - - +
4071 ARG* 3.7 32.1 - - - +
4081 PHE 4.1 8.7 - - - -
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Residues in contact with ILE 354 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2091 ILE 3.9 1.3 - - - -
3301 ILE* 6.3 1.6 - - + -
3421 MET* 4.9 12.1 - - + -
3431 ASN 5.2 0.7 - - - +
3491 HIS* 5.3 8.1 - - + +
3511 PRO* 3.4 26.7 - - + +
3521 GLY 4.8 0.7 - - - -
3531 CYS* 1.3 81.8 - - - +
3551 ASN* 1.4 61.3 + - - +
3561 LEU* 3.5 32.3 - - + -
4071 ARG* 3.8 0.3 - - - -
4081 PHE* 2.9 54.3 + - + +
4101 ILE* 4.2 21.5 - - + -
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Residues in contact with ASN 355 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2081 GLU* 3.7 16.1 + - - +
2091 ILE* 3.3 45.1 + - + +
3431 ASN* 3.0 28.4 - - - +
3541 ILE* 1.4 74.0 - - - +
3561 LEU* 1.4 66.9 + - - +
3781 GLY* 3.7 13.7 - - - -
3921 LEU* 4.3 13.6 - - - +
4051 SER* 4.8 1.2 - - - -
4061 ILE 2.8 24.6 + - - +
4071 ARG* 3.3 26.0 - - - +
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Residues in contact with LEU 356 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3401 VAL* 6.0 4.0 - - + -
3411 VAL 4.2 16.2 - - - +
3421 MET* 3.7 21.3 - - + -
3431 ASN* 3.6 19.7 - - - +
3541 ILE* 3.5 26.0 + - + -
3551 ASN* 1.4 88.0 + - - +
3571 SER* 1.4 55.9 + - - +
3581 PHE* 2.7 35.6 - - + -
3701 LEU* 6.4 0.9 - - + -
4051 SER* 4.6 0.6 - - - -
4061 ILE 3.4 16.2 + - - +
4081 PHE* 4.1 22.0 - - + -
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Residues in contact with SER 357 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3411 VAL* 3.6 34.1 - - - +
3431 ASN* 3.2 21.7 + - - -
3561 LEU* 1.4 71.2 - - - +
3581 PHE* 1.4 66.1 + - - +
3591 ALA* 3.6 14.7 - - - +
3921 LEU* 3.4 30.8 + - - +
3951 ILE* 4.5 12.2 - - - +
3971 THR* 5.5 0.5 - - - +
4051 SER* 4.2 3.1 + - - -
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Residues in contact with PHE 358 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3411 VAL* 5.3 1.2 - - - +
3561 LEU* 2.7 41.1 - - + +
3571 SER* 1.4 66.6 + - - -
3591 ALA* 1.3 60.6 + - - +
3611 VAL* 4.5 4.0 - - - -
3661 LEU* 3.9 33.4 - - + -
3671 LEU* 4.9 1.6 - - + -
3701 LEU* 3.9 37.0 - - + -
3971 THR* 5.0 0.2 - - - +
4011 LEU* 3.6 18.4 - - - +
4041 SER* 3.6 18.9 + - - +
4051 SER* 3.7 10.8 + - - -
4061 ILE* 1.4 46.0 - - + -
4081 PHE* 4.2 7.9 - + - -
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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