Contacts of the helix formed by residues 648 - 656 (chain A) in PDB entry 1XJP
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 648 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634A GLY 4.8 1.3 - - - -
635A CYS* 3.3 37.0 - - + +
640A GLU* 4.0 2.7 - - - -
641A HIS* 4.3 4.5 - - - +
644A THR* 2.8 45.6 + - - +
645A SER 4.7 0.7 - - - +
647A GLU* 1.3 75.9 - - - +
649A ASP* 1.4 65.5 + - - +
651A PRO* 3.1 5.3 - - - +
652A ILE* 2.9 48.4 + - + +
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Residues in contact with ASP 649 (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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634A GLY* 5.4 4.5 - - - -
636A LEU* 6.1 1.0 - - - +
641A HIS* 4.1 14.4 + - - -
645A SER 2.9 22.3 - - - +
646A TYR* 2.8 19.6 + - + +
648A CYS* 1.4 79.1 - - - +
650A ILE* 1.4 56.2 + - - +
652A ILE* 4.4 7.8 - - - +
653A GLY* 2.9 28.5 + - - +
656A ILE* 5.6 4.1 - - + +
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Residues in contact with ILE 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A TYR* 2.7 33.9 + - + +
647A GLU* 4.3 13.5 - - + +
649A ASP* 1.4 70.3 - - - +
651A PRO* 1.4 69.3 - - + +
654A ALA* 2.9 31.8 + - + +
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Residues in contact with PRO 651 (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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647A GLU* 2.6 40.4 - - - +
648A CYS* 3.1 9.2 - - - +
650A ILE* 1.4 94.9 - - + +
652A ILE* 1.4 59.9 + - + +
654A ALA* 4.0 5.4 - - + +
655A GLY* 3.0 21.5 + - - -
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Residues in contact with ILE 652 (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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323A CYS* 6.3 2.2 - - - -
633A ALA* 3.4 22.7 - - - +
634A GLY* 2.9 39.9 - - - +
648A CYS* 2.9 35.5 + - + +
649A ASP* 4.4 6.7 - - - +
651A PRO* 1.4 78.3 - - + +
653A GLY* 1.4 52.3 + - - +
654A ALA 3.2 0.2 - - - -
655A GLY* 3.1 5.3 - - - -
656A ILE* 2.4 46.1 + - + +
657A CYS* 5.6 0.6 - - - -
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Residues in contact with GLY 653 (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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649A ASP* 2.9 24.2 + - - +
650A ILE 3.8 0.7 - - - -
652A ILE* 1.4 66.5 - - - +
654A ALA* 1.4 58.2 + - - +
656A ILE* 2.2 49.2 + - - +
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Residues in contact with ALA 654 (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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650A ILE* 2.9 18.4 + - + +
651A PRO* 4.2 5.8 - - + +
653A GLY* 1.4 76.7 - - - +
655A GLY* 1.3 62.2 + - - +
656A ILE 3.3 0.9 + - - -
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Residues in contact with GLY 655 (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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323A CYS* 4.5 3.9 - - - -
651A PRO 3.0 16.0 + - - -
652A ILE* 3.1 8.7 - - - -
654A ALA* 1.3 74.5 - - - +
656A ILE* 1.4 49.6 + - - -
657A CYS* 2.7 32.2 + - - -
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Residues in contact with ILE 656 (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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649A ASP* 4.6 4.9 - - + +
652A ILE* 2.4 41.9 + - + +
653A GLY* 2.2 38.0 + - - +
654A ALA 3.3 4.6 + - - -
655A GLY* 1.4 65.5 - - - +
657A CYS* 1.3 66.0 + - - +
659A SER* 3.3 19.9 + - - +
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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