Contacts of the helix formed by residues 430 - 440 (chain A) in PDB entry 5XJY
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 430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425A THR 3.4 3.8 + - - -
426A PHE* 3.3 52.5 + - - -
428A GLU 3.8 1.1 - - - -
429A ASN* 1.3 76.7 - - - +
431A GLN* 1.3 62.9 + - - +
432A GLU* 3.3 17.5 + - - +
433A MET* 3.1 14.2 + - - +
434A ASP* 3.1 10.6 + - - +
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Residues in contact with GLN 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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129A LEU* 4.5 30.5 - - + +
133A GLN* 5.3 3.8 - - - +
140A SER* 4.3 25.6 - - - -
429A ASN 3.3 7.9 + - - +
430A SER* 1.3 70.0 + - - +
432A GLU* 1.3 62.9 + - - +
434A ASP* 3.2 14.3 + - + +
435A LEU* 3.1 20.6 + - - +
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Residues in contact with GLU 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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122A MET* 5.6 3.4 - - + +
125A MET* 4.3 24.5 - - + +
126A ARG* 5.8 2.0 - - - +
129A LEU* 4.7 13.9 - - + +
426A PHE* 5.0 8.7 - - + -
430A SER* 3.1 11.1 + - - +
431A GLN* 1.3 77.8 - - - +
433A MET* 1.3 59.5 + - - +
435A LEU* 3.3 9.1 + - - +
436A VAL* 3.2 18.4 + - - +
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Residues in contact with MET 433 (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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426A PHE* 3.5 37.6 - - + +
427A MET* 5.1 4.7 - - + -
430A SER* 3.1 9.8 + - - +
432A GLU* 1.3 76.2 - - - +
434A ASP* 1.3 59.5 + - - +
436A VAL* 3.2 11.0 + - + +
437A ARG* 2.9 27.4 + - - +
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Residues in contact with ASP 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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430A SER 3.1 8.4 + - - +
431A GLN* 3.3 23.1 - - + +
432A GLU 3.2 0.4 - - - -
433A MET* 1.3 77.0 - - - +
435A LEU* 1.3 57.6 + - - +
437A ARG* 3.3 8.1 + - - +
438A MET* 2.9 26.0 + - - +
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Residues in contact with LEU 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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125A MET* 3.8 21.2 - - + +
128A VAL* 5.9 4.5 - - + -
129A LEU* 6.3 2.0 - - + -
431A GLN 3.1 11.5 + - - +
432A GLU* 3.3 10.5 + - - +
434A ASP* 1.3 73.5 - - - +
436A VAL* 1.3 61.0 + - - +
438A MET* 3.4 8.8 - - + +
439A LEU* 2.9 31.7 + - - +
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Residues in contact with VAL 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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125A MET* 4.5 6.8 - - + +
265A LEU* 4.5 24.2 - - + +
432A GLU 3.2 13.1 + - - +
433A MET* 3.2 14.3 + - + +
435A LEU* 1.3 76.6 - - - +
437A ARG* 1.3 57.3 + - - +
439A LEU* 5.2 1.1 - - - -
440A LEU* 2.9 31.4 + - - +
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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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433A MET 2.9 13.5 + - - +
434A ASP* 3.6 11.2 - - - +
435A LEU 3.3 0.2 - - - -
436A VAL* 1.3 75.9 - - - +
438A MET* 1.3 63.5 + - - +
440A LEU* 3.7 13.6 + - - +
441A ASP* 4.0 6.8 + - - +
469A LYS* 5.8 4.5 - - + -
470A HIS* 3.9 26.9 - - + -
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Residues in contact with MET 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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244A ASN* 5.9 7.6 - - + -
434A ASP 2.9 14.6 + - - +
435A LEU* 3.1 14.1 + - + +
437A ARG* 1.3 77.2 - - - +
439A LEU* 1.3 59.1 + - - +
440A LEU 3.2 0.7 + - - -
441A ASP 2.9 26.5 + - - +
442A SER* 4.9 1.4 - - - -
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Residues in contact with LEU 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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125A MET* 6.1 2.5 - - + -
261A LEU* 5.9 7.4 - - + -
262A LEU* 6.3 4.0 - - + -
265A LEU* 5.4 8.7 - - + -
435A LEU 2.9 17.6 + - - +
436A VAL* 4.6 2.7 - - - +
438A MET* 1.3 71.0 - - - +
440A LEU* 1.3 64.5 + - - +
441A ASP 3.1 1.6 + - - -
442A SER* 5.6 2.5 - - - -
445A ASN* 3.4 22.0 - - + +
449A TRP* 4.6 4.3 - - - +
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Residues in contact with LEU 440 (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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265A LEU* 5.5 7.6 - - + -
436A VAL 2.9 22.5 + - - +
437A ARG* 3.8 11.2 - - - +
438A MET 3.1 0.8 - - - -
439A LEU* 1.3 77.8 - - - +
441A ASP* 1.3 59.2 + - + +
445A ASN* 4.9 3.2 - - - +
449A TRP* 5.3 5.6 - - - +
462A ASP* 4.5 18.0 - - - +
465A ALA* 5.8 1.7 - - + +
466A PHE* 5.0 13.9 - - + +
469A LYS* 5.6 7.2 - - + -
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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