Contacts of the strand formed by residues 425 - 429 (chain C) in PDB entry 1Z6T
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 PHE 425 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C PRO* 6.1 4.3 - - + -
322C LEU* 4.0 17.3 - - + -
419C VAL* 4.2 4.3 - - + -
422C SER* 4.1 13.7 - - - -
424C LEU* 1.3 82.8 - - - +
426C CYS* 1.3 62.1 + - - +
435C TYR* 3.2 9.4 - - - +
436C TYR* 2.8 74.1 + + + +
437C LEU 4.5 0.2 - - - -
438C HIS* 4.1 15.3 - + + -
441C GLN* 3.3 27.1 - - - -
902C ADP 3.1 35.0 - - - -
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Residues in contact with CYS 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C TYR* 3.5 26.0 - - + +
121C GLN* 4.1 1.0 - - - +
419C VAL* 4.0 9.0 - - + +
425C PHE* 1.3 75.6 - - - +
427C ASP* 1.3 69.7 + - - +
428C ARG* 3.0 37.7 + - - +
433C PHE* 4.0 17.3 - - - -
434C ARG 3.3 7.4 - - - -
435C TYR* 3.5 32.8 - - + -
436C TYR* 4.8 0.6 + - - -
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Residues in contact with ASP 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLY 4.7 6.8 - - - +
119C VAL 5.7 0.2 - - - -
120C PRO* 3.8 25.5 - - - +
121C GLN* 3.9 4.7 + - - +
394C LYS* 2.7 32.1 + - + +
426C CYS* 1.3 73.2 - - - +
428C ARG* 1.3 61.8 + - - +
429C ASN 4.0 0.7 + - - -
432C SER 3.7 4.2 - - - +
433C PHE* 3.8 0.9 - - - -
434C ARG* 2.9 44.1 + - + +
436C TYR* 2.9 27.3 + - + -
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Residues in contact with ARG 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C TYR* 3.5 38.0 - - + +
28C HIS* 4.4 4.0 - - - -
77C HIS* 4.3 5.1 - - - -
78C GLU* 3.0 55.9 + - - +
79C GLY* 4.7 0.9 + - - -
115C CYS* 5.2 2.8 - - - +
121C GLN* 2.9 51.5 + - - +
122C ARG 5.1 5.7 + - - -
419C VAL* 5.5 2.6 - - - +
426C CYS* 3.0 36.6 + - - +
427C ASP* 1.3 72.7 - - - +
429C ASN* 1.3 61.0 + - - +
430C GLY 3.8 0.7 - - - +
432C SER 3.8 5.2 - - - -
433C PHE* 3.7 25.6 - - + -
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Residues in contact with ASN 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C GLU 4.3 0.4 - - - -
79C GLY* 3.9 4.5 - - - +
115C CYS* 3.2 41.9 + - - +
116C GLU* 5.1 3.9 + - - +
118C GLY* 6.2 1.8 - - - -
427C ASP 4.0 1.0 + - - -
428C ARG* 1.3 71.3 - - - +
430C GLY* 1.3 63.7 + - - +
431C LYS* 3.1 4.5 + - - +
432C SER* 3.1 27.2 + - - +
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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