Contacts of the helix formed by residues 429 - 439 (chain A) in PDB entry 1YTS
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 VAL 429 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A LEU* 4.4 17.3 - - + -
419A MET* 5.6 0.7 - - - -
427A LEU 4.1 0.2 + - - -
428A SER* 1.3 70.5 - - - +
430A GLU* 1.3 64.3 + - - +
432A MET* 3.2 16.4 + - - +
433A VAL* 3.1 28.9 + - + +
451A LEU* 4.5 15.9 - - + -
454A LEU* 4.5 15.5 - - + +
455A ILE* 4.6 6.3 - - + -
458A ALA* 3.5 32.3 - - + -
463A ARG* 4.7 5.4 - - - +
464A PRO 2.8 16.7 + - - +
465A LEU* 3.9 18.4 - - + +
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Residues in contact with GLU 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LEU* 3.8 20.1 - - + +
200A ARG* 3.1 41.4 + - + +
201A LEU* 4.8 8.7 - - + -
428A SER* 3.2 4.5 - - - +
429A VAL* 1.3 69.6 - - - +
431A ASP* 1.3 58.0 + - - +
433A VAL* 4.3 0.2 - - - +
434A SER* 2.6 41.4 + - - +
465A LEU 2.7 21.8 + - - +
466A LEU* 3.6 2.3 - - - +
467A ASN* 3.1 34.2 + - - +
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Residues in contact with ASP 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A LEU* 3.9 14.8 - - + +
428A SER* 3.1 24.2 + - - +
430A GLU* 1.3 75.8 - - - +
432A MET* 1.3 59.3 + - - +
434A SER* 3.8 5.1 - - - -
435A GLN* 2.9 49.7 + - - +
467A ASN* 2.9 35.8 + - - +
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Residues in contact with MET 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A VAL* 3.5 23.4 - - + +
415A GLY* 4.1 9.6 - - - +
418A CYS* 3.2 27.4 - - - -
419A MET* 3.8 27.6 - - + +
427A LEU* 3.7 11.2 - - + +
428A SER 3.2 11.8 + - - +
429A VAL* 3.5 16.6 - - - +
431A ASP* 1.3 76.8 - - - +
433A VAL* 1.3 60.9 + - + +
435A GLN* 3.4 2.4 + - - +
436A MET* 3.0 46.4 + - + +
454A LEU* 5.4 3.1 - - - -
463A ARG* 3.3 29.4 - - - +
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Residues in contact with VAL 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 3.3 35.2 - - + -
429A VAL* 3.1 17.0 + - + +
432A MET* 1.3 71.4 - - + +
434A SER* 1.3 61.2 - - - +
435A GLN 3.2 0.3 + - - -
436A MET* 3.3 10.6 + - + +
437A ARG* 2.9 49.3 + - - +
444A MET 4.6 5.6 - - - +
445A VAL* 4.2 19.5 - - + -
451A LEU* 4.2 18.4 - - + -
454A LEU* 4.5 11.0 - - + -
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Residues in contact with SER 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A LEU* 4.0 7.5 - - - +
204A LEU* 3.8 25.2 - - - +
430A GLU* 2.6 32.8 + - - +
431A ASP* 3.8 6.3 - - - -
433A VAL* 1.3 77.2 - - - +
435A GLN* 1.4 54.4 + - - -
437A ARG* 3.4 0.7 + - - +
438A VAL* 2.9 37.9 + - - +
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Residues in contact with GLN 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A GLN 3.5 3.1 - - - +
251A VAL* 2.9 40.0 - - + +
252A GLY* 2.9 9.2 + - - +
427A LEU* 4.1 9.7 - - - +
431A ASP* 2.9 43.4 + - - +
432A MET 3.7 3.8 - - - +
433A VAL 3.3 0.4 - - - -
434A SER* 1.4 70.6 - - - +
436A MET* 1.3 70.6 + - - +
438A VAL* 3.6 3.0 + - - -
439A GLN* 3.2 44.8 + - - +
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Residues in contact with MET 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ILE* 4.2 16.2 - - + +
251A VAL* 3.7 15.2 - - + +
411A ALA* 3.8 21.3 - - - +
414A ILE* 3.6 20.6 - - + -
415A GLY* 4.1 17.5 - - - -
432A MET* 3.0 27.2 + - + +
433A VAL* 3.4 14.8 - - + +
435A GLN* 1.3 80.4 - - - +
437A ARG* 1.4 59.0 + - - +
439A GLN* 3.8 1.6 - - - +
440A ARG* 3.2 26.5 + - - +
444A MET* 3.9 31.0 - - + +
445A VAL* 4.3 15.7 - - + -
454A LEU* 4.7 2.2 - - + -
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Residues in contact with ARG 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A LEU* 2.8 44.2 + - - +
202A THR* 4.9 0.4 - - - +
204A LEU* 4.0 19.7 - - + -
205A ARG* 4.0 17.9 - - - +
208A LEU* 3.6 18.1 - - + +
217A TYR* 5.6 0.2 + - - -
235A ARG* 5.0 0.9 + - - -
433A VAL* 2.9 36.5 + - - +
434A SER 3.9 2.9 - - - +
436A MET* 1.4 66.5 - - - +
438A VAL* 1.3 65.1 + - - +
439A GLN 3.1 2.1 + - - -
440A ARG 3.9 0.3 - - - -
441A ASN* 3.3 40.9 + - - +
442A GLY* 3.2 21.8 + - - +
444A MET* 3.2 20.2 + - + +
445A VAL* 3.0 27.5 + - - +
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Residues in contact with VAL 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LEU* 4.2 22.9 - - + -
208A LEU* 4.4 7.2 - - + -
235A ARG* 3.1 41.5 + - - +
237A GLN* 3.8 13.2 + - - +
434A SER* 2.9 22.3 + - - +
435A GLN* 4.3 3.8 - - - +
437A ARG* 1.3 70.2 - - - +
439A GLN* 1.3 60.4 + - + +
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Residues in contact with GLN 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ARG* 4.0 2.5 - - - -
237A GLN* 5.5 1.8 - - - +
238A THR* 2.6 41.2 + - + +
247A ASN* 3.3 12.5 + - - +
248A TYR 4.1 7.8 - - - +
249A ILE* 3.4 10.4 - - + +
250A GLN* 2.7 50.7 + - - +
251A VAL* 4.9 0.2 - - - +
435A GLN* 3.2 39.9 + - - +
436A MET 3.9 2.0 - - - +
437A ARG 3.2 1.2 - - - -
438A VAL* 1.3 83.4 - - + +
440A ARG* 1.4 57.2 + - - +
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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