Contacts of the helix formed by residues 410 - 417 (chain A) in PDB entry 4XZC
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 HIS 410 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A MET* 5.2 0.4 - - - -
71A THR* 3.2 8.5 + - - -
332A LEU 3.3 21.1 - - - -
335A MET* 4.0 12.1 - - + +
336A GLY* 3.9 12.5 - - - -
387A SER* 4.0 10.0 + - - +
390A GLY* 3.3 33.3 + - - -
391A ALA* 3.5 22.7 - - + +
394A GLY 3.1 23.0 + - - -
395A VAL* 4.0 9.9 - - + -
408A SER* 3.2 24.0 + - - -
409A GLY* 1.3 75.3 + - - -
411A SER* 1.3 66.3 + - - +
412A LYS 3.4 0.7 - - - -
413A SER* 3.0 24.7 + - - +
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Residues in contact with SER 411 (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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67A MET* 3.7 38.8 - - - +
71A THR* 4.1 1.1 - - - -
387A SER* 4.3 20.4 + - - -
410A HIS* 1.3 67.7 - - - +
412A LYS* 1.3 62.4 + - - +
413A SER 3.0 10.5 + - - -
414A LEU* 3.0 24.8 + - - +
455A LEU* 3.9 15.7 - - - +
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Residues in contact with LYS 412 (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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305A ILE* 5.1 8.3 + - - +
307A SER* 4.0 9.8 + - - +
387A SER 5.7 2.0 + - - +
388A GLU* 2.4 42.5 + - - +
391A ALA* 4.3 11.7 - - + +
410A HIS 3.4 1.0 - - - -
411A SER* 1.3 81.8 + - - +
413A SER* 1.3 62.1 + - - +
414A LEU 3.1 0.8 + - - -
415A LEU* 3.3 23.2 + - + +
416A ASN 4.6 0.2 + - - -
454A HIS* 4.5 11.2 + - - -
455A LEU* 4.6 8.7 - - + -
458A GLN* 3.2 41.1 - - - +
463A LYS* 4.5 4.9 - - - +
466A HIS* 3.7 39.6 - - + +
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Residues in contact with SER 413 (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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71A THR* 4.0 13.9 + - - -
74A CYS* 3.5 14.5 - - - -
75A ALA* 3.4 27.5 - - - +
76A PRO* 4.6 3.5 - - - +
391A ALA* 4.5 8.4 + - - +
395A VAL* 4.5 3.8 - - - +
408A SER 5.1 0.3 + - - -
410A HIS* 3.0 27.1 + - - +
411A SER 3.0 1.0 - - - -
412A LYS* 1.3 78.7 - - - +
414A LEU* 1.3 61.6 + - - +
416A ASN* 2.9 23.4 + - - +
466A HIS* 4.6 7.5 + - - -
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Residues in contact with LEU 414 (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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67A MET* 5.2 0.4 - - - -
70A ALA* 4.6 2.7 - - + -
71A THR* 3.8 14.8 - - + +
74A CYS* 4.1 3.8 - - - -
411A SER 3.0 16.1 + - - +
413A SER* 1.3 79.3 - - - +
415A LEU* 1.3 63.6 + - + +
416A ASN 3.0 0.7 - - - -
417A TYR* 3.0 41.8 + - + +
427A CYS* 3.7 8.6 - - - +
430A GLU* 3.8 21.8 - - + -
431A ILE* 3.5 31.2 - - + -
434A LEU* 3.7 30.1 - - + -
455A LEU* 4.2 19.1 - - + -
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Residues in contact with LEU 415 (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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32A ASN* 3.4 4.2 + - - -
412A LYS* 3.6 16.6 - - + +
413A SER 3.1 1.2 + - - -
414A LEU* 1.3 79.8 - - + +
416A ASN* 1.3 60.8 + - - +
417A TYR 3.2 6.3 - - - +
427A CYS* 4.6 7.0 - - - -
455A LEU* 4.0 24.7 - - + +
458A GLN* 3.9 29.4 - - + +
459A SER* 4.3 6.5 - - - +
463A LYS* 3.7 49.5 - - + +
464A ARG* 2.9 21.6 - - - +
465A CYS* 4.1 9.0 - - - +
466A HIS* 3.9 20.2 - - + +
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Residues in contact with ASN 416 (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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31A THR* 3.2 10.9 + - - -
32A ASN* 2.7 35.6 + - - +
33A SER* 2.9 48.4 + - - -
74A CYS 2.7 22.5 + - - +
75A ALA 3.6 1.6 + - - -
76A PRO* 3.4 30.9 - - + +
412A LYS 4.6 0.2 + - - -
413A SER 2.9 15.6 + - - +
415A LEU* 1.3 76.7 - - - +
417A TYR* 1.3 59.0 + - - +
464A ARG 3.7 7.6 - - - +
465A CYS* 4.7 5.3 - - - +
466A HIS* 5.5 1.1 - - + +
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Residues in contact with TYR 417 (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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30A LEU* 3.7 14.6 - - + -
31A THR* 3.8 5.6 - - + -
32A ASN* 3.6 3.9 + - - +
37A CYS* 4.0 19.0 - - - -
40A LEU* 4.3 8.7 - - + -
41A PRO* 3.3 21.0 - - - +
70A ALA 2.7 27.8 + - - -
73A PHE 5.8 0.2 - - - -
74A CYS* 3.6 24.2 + - + +
413A SER 4.2 0.4 + - - -
414A LEU* 3.0 33.1 + - + +
415A LEU 3.4 9.0 - - - +
416A ASN* 1.3 80.4 - - - +
418A LYS* 1.3 64.8 + - - +
419A ILE* 3.5 4.0 + - - +
426A PRO* 4.5 5.8 - - + -
427A CYS* 3.5 29.8 - - - +
430A GLU* 3.4 30.1 - - + -
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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