Contacts of the helix formed by residues 410 - 417 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B MET* 4.9 0.4 - - - -
71B THR* 3.1 10.1 + - - -
332B LEU 3.2 19.9 + - - -
335B MET* 3.8 12.3 - - + +
336B GLY* 3.9 7.6 - - - -
387B SER* 4.1 8.2 + - - +
390B GLY* 3.2 35.6 + - - -
391B ALA* 3.5 21.8 - - + +
394B GLY 3.0 25.3 + - - -
395B VAL* 3.9 11.9 - - + -
408B SER* 3.2 14.6 + - - -
409B GLY* 1.3 85.4 + - - -
411B SER* 1.3 66.5 + - - +
412B LYS 3.3 1.1 - - - -
413B SER* 2.8 27.7 + - - +
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Residues in contact with SER 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B MET* 3.6 41.5 - - - +
71B THR* 3.9 0.9 - - - +
387B SER* 4.7 18.7 + - - -
410B HIS* 1.3 70.3 - - - +
412B LYS* 1.3 81.6 + - - +
413B SER 2.8 11.4 + - - -
414B LEU* 2.9 24.1 + - - +
455B LEU* 4.1 10.2 - - - +
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Residues in contact with LYS 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B ILE* 6.2 0.9 - - - -
307B SER* 4.1 9.0 - - - +
387B SER 4.8 3.5 + - - +
388B GLU* 3.0 37.5 + - - +
391B ALA* 3.7 21.2 - - + +
410B HIS 3.1 1.0 + - - -
411B SER* 1.3 94.4 + - - +
413B SER* 1.3 60.6 + - - +
414B LEU 3.1 0.8 + - - -
415B LEU* 3.5 17.6 + - + +
454B HIS* 4.7 8.1 + - - -
455B LEU* 4.6 13.1 - - - +
458B GLN* 3.5 36.9 - - - +
463B LYS* 5.2 3.6 - - - +
466B HIS* 3.7 32.6 + - + +
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Residues in contact with SER 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 4.0 6.7 - - - -
74B CYS* 3.5 15.3 - - - -
75B ALA* 3.4 33.3 - - - +
76B PRO* 4.5 6.4 - - - +
391B ALA* 4.7 5.6 + - - +
395B VAL* 4.5 5.0 - - - +
408B SER 5.3 0.5 + - - -
410B HIS* 2.8 26.4 + - - +
411B SER 2.8 0.6 + - - -
412B LYS* 1.3 77.2 - - - +
414B LEU* 1.3 54.4 + - - +
416B ASN* 2.8 35.5 + - - +
466B HIS* 5.5 3.0 + - - -
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Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B MET* 4.8 2.0 - - - -
70B ALA* 4.4 2.0 - - + +
71B THR* 3.9 12.1 - - + +
74B CYS* 4.2 4.9 - - - -
411B SER 2.9 14.8 + - - +
413B SER* 1.3 77.6 - - - +
415B LEU* 1.3 55.9 + - + +
416B ASN 3.0 5.4 + - - -
417B TYR* 3.1 54.9 + - + +
427B CYS* 3.8 8.1 - - - +
430B GLU* 3.5 17.0 - - + -
431B ILE* 4.1 24.0 - - + +
434B LEU* 3.6 24.5 - - + -
455B LEU* 3.5 30.5 - - + -
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ASN* 3.6 4.3 + - - -
412B LYS* 3.7 19.7 - - + +
413B SER 3.0 0.8 + - - -
414B LEU* 1.3 76.6 - - + +
416B ASN* 1.3 54.6 + - - +
417B TYR 3.2 4.6 + - - +
427B CYS* 4.5 7.6 - - - -
431B ILE* 6.2 0.2 - - + -
455B LEU* 3.6 40.8 - - + +
458B GLN* 3.2 35.0 - - + +
459B SER* 4.2 9.6 - - - +
463B LYS* 4.1 24.4 - - + +
464B ARG* 2.7 27.7 - - - +
465B CYS* 4.3 10.3 - - - +
466B HIS* 4.2 17.3 - - + +
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Residues in contact with ASN 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B THR* 3.0 6.8 - - - -
32B ASN* 2.4 41.5 + - - +
33B SER* 3.1 38.7 + - - -
74B CYS 2.7 25.3 + - - +
75B ALA 3.4 1.0 + - - -
76B PRO* 3.3 36.8 - - + +
144B TYR* 5.6 0.3 - - - -
412B LYS 4.9 0.2 + - - -
413B SER 2.8 16.4 + - - +
415B LEU* 1.3 76.5 - - - +
417B TYR* 1.3 59.0 + - - +
464B ARG 3.7 6.5 - - - +
465B CYS* 4.9 5.2 - - - +
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Residues in contact with TYR 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 3.7 10.1 - - + -
31B THR* 3.6 13.0 - - + +
32B ASN* 3.6 7.0 + - - -
37B CYS* 3.6 20.2 - - - -
40B LEU* 4.4 7.2 - - + -
41B PRO* 3.2 22.0 - - + +
70B ALA 2.7 29.5 + - - -
73B PHE 5.8 0.2 + - - -
74B CYS* 3.3 27.3 + - + +
413B SER 4.4 0.2 + - - -
414B LEU* 3.1 41.3 + - + +
415B LEU 3.7 3.8 - - - +
416B ASN* 1.3 80.2 - - - +
418B LYS* 1.3 66.5 + - - +
419B ILE* 4.4 2.6 - - - +
426B PRO* 4.1 8.7 - - + -
427B CYS* 3.2 29.5 - - - +
430B GLU* 3.6 14.6 - - + -
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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