Contacts of the helix formed by residues 412 - 422 (chain A) in PDB entry 4X2Q
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 THR 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A PHE* 3.3 22.0 - - - -
411A LYS* 1.3 105.5 - - + +
413A MET* 1.3 62.9 + - - +
414A ASP* 3.9 8.0 + - - +
415A GLU* 3.4 30.1 + - - +
416A VAL* 3.7 1.0 - - - +
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Residues in contact with MET 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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278A PHE* 4.1 24.9 - - + -
412A THR* 1.3 71.3 - - - +
414A ASP* 1.3 65.7 + - - +
415A GLU 3.1 5.8 + - - -
416A VAL* 3.3 19.9 - - - +
417A ILE* 3.4 19.8 - - + +
437A ASN 5.6 0.9 - - - +
438A LYS* 3.7 37.7 - - + -
441A THR* 3.5 31.0 - - - -
442A VAL* 4.4 7.2 - - + -
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Residues in contact with ASP 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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412A THR* 3.4 7.4 + - - +
413A MET* 1.3 79.0 - - - +
415A GLU* 1.3 61.1 + - - +
417A ILE* 4.3 10.4 - - - +
418A GLU* 3.0 34.1 + - - +
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Residues in contact with GLU 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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409A ARG 3.7 2.3 - - - +
410A PHE* 3.4 16.8 - - + -
411A LYS* 2.8 38.3 + - - +
412A THR* 3.4 22.0 + - - +
413A MET 3.1 0.6 - - - -
414A ASP* 1.3 76.7 - - - +
416A VAL* 1.3 66.7 + - - +
418A GLU* 3.3 5.0 + - - +
419A ARG* 3.0 53.0 + - + +
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Residues in contact with VAL 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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276A ILE* 3.9 23.8 - - + -
278A PHE* 4.7 5.8 - - + -
309A PHE* 3.7 26.7 - - + -
410A PHE* 3.4 44.2 - - + -
412A THR 3.7 11.4 - - - +
413A MET* 3.3 21.1 - - - +
415A GLU* 1.3 74.8 - - - +
417A ILE* 1.3 56.6 + - + +
419A ARG* 4.4 5.2 - - - +
420A ALA* 2.6 40.3 + - - +
442A VAL* 5.6 0.9 - - + -
446A MET* 5.2 0.4 - - - -
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Residues in contact with ILE 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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276A ILE* 6.0 0.2 - - + -
413A MET* 3.4 29.1 + - + +
414A ASP* 4.5 8.5 - - - +
415A GLU 3.3 0.6 - - - -
416A VAL* 1.3 76.7 - - + +
418A GLU* 1.3 68.8 + - - +
421A ASN* 3.0 48.4 + - - +
441A THR* 4.4 14.6 - - + +
442A VAL* 4.3 21.3 - - + -
445A ALA* 3.8 24.5 - - + +
446A MET* 4.0 25.3 - - + +
72B LEU* 5.6 3.1 - - + -
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Residues in contact with GLU 418 (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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414A ASP* 3.0 34.5 + - - +
415A GLU* 3.3 4.1 + - - +
416A VAL 3.3 0.2 - - - -
417A ILE* 1.3 87.0 - - - +
419A ARG* 1.3 64.7 + - + +
421A ASN* 4.2 6.2 + - - +
422A ASN* 3.4 23.2 + - - +
72B LEU* 4.7 15.1 - - - +
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Residues in contact with ARG 419 (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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272A LYS* 3.4 12.0 + - - -
307A ARG* 4.0 4.3 + - - -
309A PHE* 3.2 36.9 - - + -
389A VAL 5.0 3.6 + - - -
390A THR* 5.1 3.4 - - - +
391A ASP* 2.7 53.1 + - - +
408A LEU* 4.4 5.9 - - - +
409A ARG 2.5 32.8 + - - +
410A PHE* 3.5 7.7 - - - +
415A GLU* 3.0 43.4 + - + +
416A VAL* 3.8 4.2 - - - +
418A GLU* 1.3 80.4 - - + +
420A ALA* 1.3 62.1 + - - +
422A ASN* 3.8 10.0 + - - +
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Residues in contact with ALA 420 (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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272A LYS* 2.8 27.6 + - - +
274A PRO* 3.8 25.7 - - + +
276A ILE* 4.5 7.6 - - + -
309A PHE* 4.2 11.4 - - + -
416A VAL 2.6 21.7 + - - +
419A ARG* 1.3 72.7 - - - +
421A ASN* 1.3 60.7 + - - +
422A ASN 3.3 0.4 - - - -
427A LEU* 3.8 11.0 - - - +
446A MET* 3.9 16.8 - - - -
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Residues in contact with ASN 421 (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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417A ILE* 3.0 29.6 + - - +
418A GLU* 4.2 9.4 + - - +
420A ALA* 1.3 76.1 - - - +
422A ASN* 1.3 53.1 + - - +
423A SER* 2.6 26.7 + - - +
427A LEU* 4.5 6.3 - - - +
445A ALA 3.1 21.2 + - - -
446A MET* 3.3 13.1 - - - +
447A GLN* 2.8 59.2 + - - +
72B LEU* 4.9 8.7 - - - +
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Residues in contact with ASN 422 (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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272A LYS* 3.5 13.4 + - - +
391A ASP* 5.5 5.6 + - - +
418A GLU 3.4 17.3 + - - +
419A ARG* 3.9 9.2 - - - +
420A ALA 3.3 1.8 - - - -
421A ASN* 1.3 71.6 - - - +
423A SER* 1.3 59.1 + - - +
424A ASP* 5.5 2.1 - - - +
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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