Contacts of the helix formed by residues 568 - 579 (chain H) in PDB entry 4D1Q
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 SER 568 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178H THR* 3.3 19.5 - - - -
179H ILE 4.7 8.3 - - - -
180H ASP* 4.8 0.8 + - - -
246H VAL* 3.8 9.3 - - - +
247H THR* 4.6 7.9 - - - -
248H ASP* 4.6 2.8 - - - +
265H CYS* 3.4 10.8 - - - +
268H HIS* 3.3 31.0 + - - -
567H SER* 1.3 73.0 - - - +
569H ALA* 1.3 64.9 + - - +
570H ALA 3.1 2.2 - - - -
571H SER* 3.0 14.5 + - - -
572H GLU* 3.2 18.4 + - - +
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Residues in contact with ALA 569 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265H CYS* 5.0 1.0 - - - -
319H TRP* 5.2 3.5 - - + -
375H GLN* 3.7 23.6 - - + +
377H CYS* 5.6 0.7 - - - -
567H SER* 3.1 19.0 + - - +
568H SER* 1.3 75.8 - - - +
570H ALA* 1.3 57.9 + - - +
572H GLU* 3.1 9.4 + - - +
573H ARG* 2.8 55.4 + - - +
16L G 4.2 10.7 + - - +
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Residues in contact with ALA 570 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178H THR* 3.8 7.6 - - + +
195H THR* 3.9 10.8 - - + +
197H HIS* 3.4 37.0 - - + +
206H ASP* 4.1 2.5 - - - +
377H CYS* 3.9 6.7 - - - -
565H PRO* 6.0 0.2 - - + -
567H SER 4.3 1.8 + - - +
568H SER 3.1 1.0 - - - -
569H ALA* 1.3 79.4 - - - +
571H SER* 1.3 61.3 + - - +
573H ARG* 3.3 23.8 + - - +
574H THR* 3.2 23.0 + - - -
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Residues in contact with SER 571 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178H THR* 3.1 13.5 + - - -
179H ILE* 3.0 29.2 + - - -
180H ASP* 4.0 23.1 - - - -
193H GLY 4.1 6.0 + - - -
195H THR* 3.2 6.0 + - - -
568H SER* 3.0 10.3 + - - -
570H ALA* 1.3 74.6 - - - +
572H GLU* 1.3 71.6 + - - +
574H THR* 3.0 21.0 + - - -
575H PHE* 3.2 15.3 + - - -
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Residues in contact with GLU 572 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180H ASP* 3.0 31.6 - - - +
268H HIS* 3.4 19.6 + - - -
319H TRP* 4.6 4.5 - - + -
568H SER* 3.3 21.0 + - - +
569H ALA* 3.1 7.1 + - - +
571H SER* 1.3 74.1 - - - +
573H ARG* 1.3 54.2 + - - +
575H PHE* 2.8 42.9 + - - +
576H SER 3.3 3.1 + - - -
15L T 3.7 12.1 + - + +
16L G 2.7 64.9 + - + +
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Residues in contact with ARG 573 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206H ASP* 4.0 11.3 + - - -
375H GLN 2.5 30.9 + - - -
377H CYS* 3.8 12.3 - - - -
569H ALA* 2.8 29.4 + - - +
570H ALA* 3.3 31.4 + - - +
572H GLU* 1.3 71.7 - - - +
574H THR* 1.3 60.8 + - - +
576H SER* 3.1 15.0 + - - -
577H LEU* 3.2 18.9 + - + +
1K A 3.1 36.3 + - + -
2K G 2.8 57.2 + - - +
3K A 5.9 0.2 - - - -
15L T 3.6 8.9 + - - +
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Residues in contact with THR 574 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193H GLY* 4.9 6.3 - - - -
194H VAL 5.6 1.2 - - - +
195H THR* 4.4 4.2 - - - +
208H ILE* 3.1 43.7 - - + +
211H LEU* 4.7 9.0 - - + -
570H ALA 3.2 12.5 + - - -
571H SER* 3.0 16.2 + - - +
572H GLU 2.9 0.2 + - - -
573H ARG* 1.3 73.1 - - - +
575H PHE* 1.3 79.9 + - + +
577H LEU* 2.9 21.1 + - - +
578H ALA* 2.9 10.9 + - - +
598H LEU* 4.5 14.3 - - + +
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Residues in contact with PHE 575 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180H ASP* 3.6 47.8 - - + -
181H LEU 3.8 10.5 - - - -
182H TRP* 3.4 56.6 - + + +
193H GLY* 4.0 21.8 - - - -
211H LEU* 4.1 9.4 - - + -
571H SER* 3.6 20.2 - - - -
572H GLU* 2.8 24.0 + - - +
574H THR* 1.3 77.2 - - + +
576H SER* 1.3 62.2 + - - +
578H ALA* 2.9 18.5 + - - +
579H GLY* 3.0 10.7 + - - -
15L T 4.2 14.4 - - - +
16L G 4.7 0.7 - - - -
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Residues in contact with SER 576 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572H GLU 3.3 2.4 + - - -
573H ARG 3.1 13.4 + - - -
575H PHE* 1.3 78.6 - - - +
577H LEU* 1.3 63.5 + - - +
579H GLY* 3.5 6.2 + - - -
580H ASN* 3.1 25.6 + - - +
2K G 3.8 11.2 + - - -
3K A 4.7 4.9 + - - -
14L C 2.6 37.2 + - - -
15L T 3.4 20.5 + - - -
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Residues in contact with LEU 577 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208H ILE* 5.2 12.6 - - + -
573H ARG* 3.4 16.6 - - + +
574H THR* 2.9 13.0 + - - +
576H SER* 1.3 77.7 - - - +
578H ALA* 1.3 64.5 + - - +
579H GLY 3.0 2.0 - - - -
580H ASN* 2.9 26.4 + - - +
581H ILE* 3.3 16.0 + - + +
598H LEU* 3.9 17.7 - - + +
601H ASN* 4.8 11.4 - - + +
605H LYS* 4.6 17.3 - - - +
2K G 5.7 0.2 - - - +
3K A 3.6 40.6 - - + +
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Residues in contact with ALA 578 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182H TRP* 3.5 25.8 - - + -
211H LEU* 3.7 23.3 - - + -
574H THR 2.9 11.1 + - - +
575H PHE* 2.9 11.0 + - - +
577H LEU* 1.3 76.0 - - - +
579H GLY* 1.3 60.3 + - - +
581H ILE* 3.4 14.7 + - - +
582H ILE* 3.5 22.6 - - + +
594H VAL* 4.7 3.4 - - + -
598H LEU* 3.9 12.5 - - + +
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Residues in contact with GLY 579 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584G GLU* 5.2 5.5 - - - +
585G LYS* 5.3 0.5 - - - -
182H TRP* 4.1 13.4 - - - -
575H PHE 3.0 11.5 + - - -
576H SER 3.5 4.5 + - - -
577H LEU 3.0 0.4 - - - -
578H ALA* 1.3 75.3 - - - +
580H ASN* 1.3 66.1 + - - +
581H ILE 3.2 1.6 - - - -
582H ILE* 3.7 18.4 + - - +
583H THR* 4.3 2.8 + - - -
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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
------------------------------------------------------------
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