Contacts of the helix formed by residues 441 - 446 (chain A) in PDB entry 2XQJ
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 GLU 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A GLU* 3.2 21.8 - - - +
223A GLN* 2.9 33.8 + - - +
224A SER* 4.5 3.7 + - - -
322A ASN* 3.0 25.7 + - - +
419A TYR* 4.3 12.8 - - + +
421A PHE* 3.7 38.6 - - + -
439A GLY* 3.4 6.1 + - - -
440A TYR* 1.4 78.5 + - - +
442A ILE* 1.3 65.1 + - - +
443A GLU 3.3 1.8 - - - -
444A PHE* 2.8 23.3 + - - +
445A VAL* 3.0 17.8 + - + +
471A TRP* 6.1 0.2 - - + -
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Residues in contact with ILE 442 (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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82A TRP* 4.0 15.0 - - + -
112A TRP* 4.4 2.2 - - + -
127A VAL* 3.5 26.2 - - + +
128A TYR* 3.7 25.4 - - + +
197A GLU* 3.7 36.8 - - + +
223A GLN* 4.2 4.0 - - - +
439A GLY* 3.5 18.8 - - - +
440A TYR 3.4 1.6 - - - -
441A GLU* 1.3 95.1 - - - +
443A GLU* 1.3 64.9 + - - +
445A VAL* 2.9 10.0 + - - +
446A PHE* 2.9 34.9 + - + -
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Residues in contact with GLU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A MET* 4.8 4.7 - - - +
127A VAL* 4.5 18.2 - - + +
425A SER* 3.6 11.6 + - - -
427A LYS* 5.4 0.7 - - - +
439A GLY 4.8 0.9 + - - +
440A TYR* 3.5 26.9 - - - +
442A ILE* 1.3 79.8 - - - +
444A PHE* 1.3 76.5 + - + +
446A PHE 4.0 0.6 - - - +
447A GLY 3.2 2.3 + - - -
448A LEU* 3.1 43.2 + - + -
449A PRO* 3.3 2.9 - - + +
456A TYR* 2.3 43.4 + - + +
1533A NA 3.0 26.5 - - - -
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Residues in contact with PHE 444 (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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421A PHE* 4.0 11.0 - + + -
423A HIS* 3.7 27.6 - + - -
425A SER* 4.4 12.6 - - - -
440A TYR 3.9 15.9 - - - -
441A GLU 2.8 12.4 + - - +
443A GLU* 1.3 89.6 - - + +
445A VAL* 1.3 65.5 + - - +
447A GLY* 3.1 3.8 + - - -
449A PRO* 3.8 13.5 - - + -
456A TYR* 4.5 2.7 - + - -
460A GLU* 3.8 37.7 - - + -
463A LEU* 4.3 11.9 - - + -
464A SER* 2.8 45.0 + - - +
467A ILE* 4.1 20.7 - - + +
468A VAL* 3.7 5.4 - - - +
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Residues in contact with VAL 445 (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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133A LEU* 3.7 10.9 - - + +
195A PHE* 3.9 19.5 - - + -
223A GLN* 3.7 23.1 - - - +
441A GLU* 3.0 18.5 + - + +
442A ILE* 2.9 9.7 + - - +
444A PHE* 1.3 77.0 - - + +
446A PHE* 1.3 62.6 + - + +
447A GLY 3.4 0.7 + - - -
467A ILE* 3.9 15.9 - - + -
468A VAL* 3.4 16.5 - - - +
471A TRP* 3.6 51.0 - - + +
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Residues in contact with PHE 446 (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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112A TRP* 3.5 53.6 - + + -
127A VAL 3.3 23.1 - - - +
128A TYR* 3.4 24.2 - - - -
129A ASP 3.6 19.9 - - - +
130A GLY* 4.2 5.8 - - - -
132A PHE* 3.2 23.9 - - - +
133A LEU* 3.9 22.6 + - + +
141A VAL* 4.7 6.1 - - + -
195A PHE* 3.7 19.1 - + - -
442A ILE* 2.9 27.5 + - + +
445A VAL* 1.3 78.8 - - + +
447A GLY* 1.3 63.6 + - - +
448A LEU* 3.4 13.1 + - + -
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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