Contacts of the strand formed by residues 432 - 436 (chain D) 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 SER 432 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427D ASP 3.7 1.7 - - - +
428D ARG* 3.7 1.4 - - - -
429D ASN* 3.0 42.3 + - - +
431D LYS* 1.3 86.0 - - - +
433D PHE* 1.3 62.0 + - - +
434D ARG* 5.3 8.9 + - - -
478D GLU* 5.0 11.0 + - - -
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Residues in contact with PHE 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LYS* 3.6 34.4 - - + +
23D SER* 4.2 6.1 - - - -
24D TYR* 3.4 34.3 - + + -
78D GLU* 5.4 0.4 - - - -
80D TYR* 4.9 0.4 - - - -
396D PRO* 3.5 2.4 - - - +
397D THR* 3.4 35.8 + - - +
412D GLU* 3.6 22.9 - - + +
426D CYS* 4.2 8.5 - - - -
427D ASP 3.8 2.7 - - - -
428D ARG* 3.6 15.5 - - + -
430D GLY 3.6 18.6 - - - -
431D LYS 3.4 7.3 + - - -
432D SER* 1.3 79.6 - - - +
434D ARG* 1.3 66.0 + - - +
435D TYR* 3.4 25.1 - - + +
478D GLU* 5.0 3.8 + - - +
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Residues in contact with ARG 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D GLY* 5.8 6.5 + - - -
201D ASN* 5.5 5.3 + - - +
205D ARG* 6.1 2.6 - - - +
394D LYS* 3.9 47.2 + - + +
395D VAL 3.4 4.7 - - - +
396D PRO* 4.1 19.1 - - + -
425D PHE 4.0 0.2 - - - +
426D CYS* 3.3 3.9 - - - -
427D ASP* 2.9 52.0 + - + +
429D ASN* 5.6 7.9 - - - +
432D SER* 5.3 9.0 + - - -
433D PHE* 1.3 81.4 - - - +
435D TYR* 1.3 63.7 + - - +
436D TYR* 4.1 3.6 - - - -
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Residues in contact with TYR 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D TYR* 4.4 6.3 + - - -
389D LEU* 4.3 6.8 - - + +
393D VAL 3.8 1.7 - - - +
394D LYS* 3.4 0.7 - - - -
395D VAL* 2.9 43.7 + - + +
397D THR* 3.5 22.9 - - - -
400D LEU* 4.2 13.2 - - + -
412D GLU* 3.5 20.4 + - - +
415D LEU* 3.3 39.0 - - + +
419D VAL* 4.4 2.2 - - + -
424D LEU* 3.8 25.4 - - + -
425D PHE 3.2 13.7 - - - +
426D CYS* 3.6 25.4 - - + -
433D PHE* 3.4 27.1 - - + -
434D ARG* 1.3 75.0 - - - +
436D TYR* 1.3 64.2 + - - +
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Residues in contact with TYR 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D PRO* 4.3 10.0 - - - +
389D LEU* 4.5 5.2 - - - -
392D ASP* 6.2 1.3 - - - +
393D VAL 3.8 17.5 - - - +
394D LYS* 3.7 34.6 + - + -
424D LEU* 3.5 5.9 - - - +
425D PHE* 2.8 66.8 + + + +
426D CYS 4.9 0.7 + - - -
427D ASP* 3.0 46.2 + - - -
434D ARG 4.1 3.4 - - - -
435D TYR* 1.3 79.1 - - - +
437D LEU* 1.3 76.1 + - - +
438D HIS* 6.1 0.4 - - - -
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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