Contacts of the helix formed by residues 568 - 582 (chain E) in PDB entry 6DWZ
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178E THR* 3.6 13.7 - - - -
179E ILE 4.5 1.5 + - - -
180E ASP* 3.7 18.5 + - - +
246E VAL 5.0 1.1 - - - -
247E THR* 4.5 13.5 - - - -
248E ASP 4.6 0.4 - - - -
265E CYS* 3.6 25.0 - - - +
268E HIS* 3.5 21.4 - - - -
567E SER* 1.3 72.3 + - - +
569E ALA* 1.3 56.9 + - - +
570E ALA 3.3 2.2 - - - -
571E SER* 3.0 26.0 + - - -
572E GLU* 3.5 7.5 + - - +
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Residues in contact with ALA 569 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267E SER* 5.5 0.8 + - - +
318E ARG* 4.7 8.7 - - - +
319E TRP* 5.9 0.7 - - + -
375E GLN* 3.5 30.1 - - + +
567E SER* 3.0 16.7 + - - +
568E SER* 1.3 73.1 - - - +
570E ALA* 1.3 67.2 + - - +
571E SER 2.9 2.5 - - - -
572E GLU* 2.7 24.8 + - - +
573E ARG* 2.8 27.9 + - + +
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Residues in contact with ALA 570 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E THR* 4.4 5.4 - - + +
195E THR* 3.8 13.4 - - + +
197E HIS* 3.7 28.9 - - + +
206E ASP* 3.8 9.4 - - - +
377E CYS* 4.1 7.2 - - - -
568E SER 3.3 0.6 - - - -
569E ALA* 1.3 76.2 - - - +
571E SER* 1.3 61.8 + - - +
573E ARG* 3.3 29.2 + - - +
574E THR* 3.1 23.9 + - - -
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Residues in contact with SER 571 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E THR* 2.9 33.5 + - - +
179E ILE* 3.5 7.6 - - - -
180E ASP* 3.7 22.0 + - - -
193E GLY* 4.1 6.7 + - - -
195E THR* 4.6 3.2 - - - +
568E SER* 3.0 15.3 + - - -
569E ALA 2.9 0.8 - - - -
570E ALA* 1.3 77.4 - - - +
572E GLU* 1.3 64.3 + - - +
574E THR* 3.2 10.3 - - - -
575E PHE* 3.1 30.2 + - - -
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Residues in contact with GLU 572 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E ASP* 3.0 28.0 - - - +
268E HIS* 4.3 11.2 + - - -
318E ARG* 3.6 39.3 + - - +
319E TRP* 4.5 5.4 - - - -
568E SER* 3.5 12.4 + - - -
569E ALA* 2.7 19.9 + - - +
571E SER* 1.3 75.0 - - - +
573E ARG* 1.3 56.9 + - - +
575E PHE* 3.0 17.5 + - + +
576E SER* 2.8 30.1 + - - -
17G G 5.7 0.5 - - - +
7H C 5.4 0.7 - - - +
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Residues in contact with ARG 573 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206E ASP* 4.3 11.5 + - - -
375E GLN* 2.4 33.9 + - - +
376E THR* 4.2 1.6 - - - +
377E CYS* 3.3 28.4 - - - +
378E SER 5.8 0.2 - - - -
569E ALA* 2.8 21.6 + - + +
570E ALA* 3.3 33.3 - - - +
572E GLU* 1.3 76.3 - - + +
574E THR* 1.3 63.7 + - - +
576E SER* 3.2 9.8 + - - -
577E LEU* 3.0 30.7 + - + +
2F G 5.3 14.5 + - - +
3F A 5.2 11.6 + - - +
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Residues in contact with THR 574 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E GLY* 5.3 5.4 - - - -
194E VAL 5.7 0.7 - - - +
195E THR* 3.9 6.9 - - + +
208E ILE* 3.3 35.0 - - + +
210E GLY 5.4 0.7 - - - +
211E LEU* 4.8 11.2 - - + -
570E ALA 3.1 11.4 + - - -
571E SER* 3.2 12.3 + - - +
573E ARG* 1.3 77.3 - - - +
575E PHE* 1.4 66.9 + - + +
577E LEU* 3.2 16.7 - - - +
578E ALA* 2.8 25.8 + - - +
598E LEU* 4.0 20.2 - - + +
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Residues in contact with PHE 575 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E ASP* 3.6 46.0 - - + -
181E LEU 4.1 4.5 - - - -
182E TRP* 3.4 63.3 - + + +
191E PHE 5.0 0.7 - - - -
193E GLY* 3.9 11.7 - - - -
211E LEU* 3.7 28.3 - - + -
571E SER* 3.4 18.4 - - - -
572E GLU* 3.0 22.9 + - + +
574E THR* 1.4 74.6 - - + +
576E SER* 1.3 69.0 + - - +
578E ALA* 2.8 17.2 + - - +
579E GLY* 2.9 11.6 + - - -
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Residues in contact with SER 576 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572E GLU 2.8 15.4 + - - -
573E ARG* 3.4 12.6 - - - -
575E PHE* 1.3 74.8 - - - +
577E LEU* 1.3 56.0 + - - +
579E GLY* 3.1 9.4 + - - -
580E ASN* 2.7 28.0 + - - -
2F G 5.0 10.9 + - - -
3F A 4.7 20.3 + - - -
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Residues in contact with LEU 577 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E ILE* 4.0 28.0 - - + -
573E ARG* 3.0 21.8 + - + +
574E THR* 3.2 8.1 - - - +
576E SER* 1.3 75.4 - - - +
578E ALA* 1.3 57.2 + - - +
580E ASN* 2.9 28.6 + - - +
581E ILE* 3.2 16.8 + - + +
598E LEU* 4.0 12.1 - - + -
601E ASN* 4.3 20.6 - - + +
605E LYS* 4.6 17.5 - - - +
3F A 5.5 6.7 - - - +
4F G 4.7 14.1 - - - +
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Residues in contact with ALA 578 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E TRP* 4.0 16.8 - - + -
211E LEU* 4.0 15.5 - - + -
574E THR 2.8 12.9 + - - +
575E PHE* 2.8 17.0 + - - +
577E LEU* 1.3 71.2 - - - +
579E GLY* 1.3 58.8 + - - +
580E ASN 3.2 0.2 - - - -
581E ILE* 3.3 10.7 + - - +
582E ILE* 3.0 32.7 + - + +
594E VAL* 4.9 4.3 - - + -
598E LEU* 3.9 18.1 - - + +
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Residues in contact with GLY 579 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E TRP* 4.2 16.1 - - - -
575E PHE 2.9 11.4 + - - -
576E SER 3.1 5.1 + - - -
578E ALA* 1.3 75.0 - - - +
580E ASN* 1.3 64.2 + - - +
581E ILE 3.3 0.2 - - - -
582E ILE 3.5 20.5 - - - +
583E THR* 4.2 3.6 - - - +
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Residues in contact with ASN 580 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A CYS* 4.1 20.1 - - - -
585A LYS* 3.2 35.9 - - + +
576E SER* 2.7 35.8 + - - -
577E LEU* 2.9 13.5 + - - +
579E GLY* 1.3 77.0 - - - +
581E ILE* 1.3 64.8 + - - +
583E THR* 3.4 12.5 - - - +
586E ARG* 4.5 3.3 + - - -
3F A 5.8 5.7 + - - -
4F G 5.2 4.9 - - - +
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Residues in contact with ILE 581 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A CYS* 3.3 31.4 - - + -
577E LEU* 3.2 14.6 + - + +
578E ALA* 3.5 12.3 - - - +
579E GLY 3.3 0.2 - - - -
580E ASN* 1.3 79.8 - - - +
582E ILE* 1.3 61.2 + - + +
583E THR* 3.1 13.0 + - - +
586E ARG* 3.4 38.9 - - - +
589E ILE* 4.2 9.2 - - + +
594E VAL* 4.0 23.6 - - + -
597E LEU* 4.8 19.3 - - + -
598E LEU* 4.2 18.4 - - + -
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Residues in contact with ILE 582 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E TRP* 4.2 12.3 - - + -
184E ASP* 4.2 38.2 - - + +
186E TYR* 3.7 18.9 - - + -
187E ILE* 5.8 1.8 - - + -
191E PHE* 4.7 11.2 - - + -
211E LEU* 6.3 0.2 - - + -
578E ALA* 3.0 19.8 + - + +
579E GLY* 3.5 13.2 - - - +
580E ASN 3.5 0.6 - - - -
581E ILE* 1.3 74.9 - - - +
583E THR* 1.3 63.4 + - - +
586E ARG* 4.8 2.9 - - - -
587E ASN* 4.9 12.3 - - - +
589E ILE* 4.5 11.9 - - + -
594E VAL* 4.0 31.2 - - + -
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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