Contacts of the helix formed by residues 568 - 582 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A THR* 4.3 11.0 - - - -
179A ILE 4.6 8.1 - - - -
180A ASP* 4.1 4.9 + - - -
246A VAL* 4.4 2.2 - - - -
247A THR* 4.3 8.3 - - - -
248A ASP* 4.3 11.4 + - - -
265A CYS* 3.2 19.9 - - - +
268A HIS* 3.1 25.0 - - - -
567A SER* 1.3 71.8 - - - +
569A ALA* 1.3 63.6 + - - +
570A ALA 3.2 4.0 + - - -
571A SER* 3.2 20.0 + - - -
572A GLU* 3.5 13.6 + - - +
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Residues in contact with ALA 569 (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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267A SER* 5.0 2.1 + - - +
318A ARG* 5.7 2.9 - - - +
375A GLN* 3.5 37.5 - - + +
567A SER* 3.1 19.6 + - - +
568A SER* 1.3 74.8 - - - +
570A ALA* 1.3 56.3 + - - +
572A GLU* 2.9 13.2 + - - +
573A ARG* 2.7 46.7 + - + +
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Residues in contact with ALA 570 (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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178A THR* 3.5 8.5 - - + +
195A THR* 3.4 29.8 - - + +
197A HIS* 3.8 14.8 - - + +
206A ASP* 4.0 5.2 - - - +
377A CYS* 4.5 1.3 - - - -
567A SER 4.5 1.8 + - - +
568A SER 3.2 0.8 + - - -
569A ALA* 1.3 77.2 - - - +
571A SER* 1.3 52.6 + - - +
573A ARG* 3.0 27.6 + - - +
574A THR* 2.7 39.8 + - - -
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Residues in contact with SER 571 (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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178A THR* 3.4 26.0 + - - -
179A ILE* 3.6 12.0 + - - -
180A ASP* 3.7 23.9 + - - -
193A GLY* 4.3 7.3 + - - -
195A THR* 4.2 4.3 - - - +
568A SER 3.2 11.3 + - - -
570A ALA* 1.3 76.9 - - - +
572A GLU* 1.3 58.4 + - - -
574A THR* 2.9 11.4 + - - -
575A PHE* 2.7 38.8 + - - -
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Residues in contact with GLU 572 (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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180A ASP* 2.7 28.9 - - - +
268A HIS* 4.0 17.9 + - - -
318A ARG* 3.5 38.2 + - - +
319A TRP* 4.3 3.5 - - - -
568A SER* 3.5 15.6 + - - -
569A ALA* 2.9 13.9 + - - +
571A SER* 1.3 77.4 - - - +
573A ARG* 1.3 65.2 + - + +
575A PHE* 2.8 27.2 + - + +
576A SER* 2.8 14.6 + - - -
7D C 5.3 0.3 - - - +
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Residues in contact with ARG 573 (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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206A ASP* 3.7 16.4 + - - -
375A GLN* 3.7 12.7 + - - +
377A CYS* 2.9 43.5 - - - +
569A ALA* 2.7 23.9 + - + +
570A ALA* 3.3 34.4 + - - +
572A GLU* 1.3 72.1 - - + +
574A THR* 1.3 62.9 + - - +
576A SER* 3.2 19.8 - - - -
577A LEU* 3.3 16.0 + - + +
2B G 5.2 7.9 - - - +
3B A 4.5 17.5 - - - +
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Residues in contact with THR 574 (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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193A GLY* 5.6 5.2 - - - -
194A VAL 6.0 0.9 - - - +
195A THR* 3.8 7.8 - - + +
208A ILE* 3.2 40.2 - - + +
210A GLY 6.0 0.4 - - - +
211A LEU* 5.1 9.2 - - + -
570A ALA 2.7 17.9 + - - -
571A SER* 3.1 13.2 - - - +
573A ARG* 1.3 73.6 - - - +
575A PHE* 1.3 71.3 + - + +
577A LEU* 3.0 22.1 + - - +
578A ALA* 3.0 11.3 + - + +
598A LEU* 4.2 17.2 - - + +
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Residues in contact with PHE 575 (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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180A ASP* 3.4 48.0 - - + -
181A LEU 3.8 8.5 - - - -
182A TRP* 3.3 57.1 - + + +
193A GLY* 4.1 11.4 - - - -
211A LEU* 3.7 26.5 - - + -
571A SER* 2.7 30.2 + - - -
572A GLU* 2.8 16.7 + - + +
574A THR* 1.3 72.0 - - + +
576A SER* 1.3 66.9 + - - +
578A ALA* 3.1 7.8 + - + +
579A GLY* 2.9 20.6 + - - -
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Residues in contact with SER 576 (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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572A GLU 2.8 11.0 + - - -
573A ARG* 3.2 15.7 - - - -
575A PHE* 1.3 78.1 - - - +
577A LEU* 1.3 53.1 + - - +
579A GLY* 3.3 7.4 + - - -
580A ASN* 2.7 28.2 + - - +
2B G 5.9 2.1 + - - -
3B A 4.3 22.7 + - - -
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Residues in contact with LEU 577 (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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208A ILE* 5.4 7.6 - - + -
573A ARG* 3.7 14.6 - - + +
574A THR* 3.0 13.6 + - - +
576A SER* 1.3 74.8 - - - +
578A ALA* 1.3 66.6 + - - +
579A GLY 3.1 1.6 - - - -
580A ASN* 3.1 21.8 + - - +
581A ILE* 3.3 16.5 + - - +
598A LEU* 4.1 15.7 - - + -
601A ASN* 5.0 10.1 - - - +
605A LYS* 4.9 16.8 - - - +
3B A 4.7 10.8 - - - +
4B G 4.7 15.0 - - - +
106E CYS* 5.2 3.5 - - + -
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Residues in contact with ALA 578 (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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182A TRP* 4.0 21.8 - - + -
211A LEU* 4.1 9.4 - - + -
574A THR 3.0 11.4 + - - +
575A PHE* 3.1 11.6 + - - +
577A LEU* 1.3 75.2 - - - +
579A GLY* 1.3 57.8 + - - +
581A ILE* 3.0 8.5 + - - +
582A ILE* 2.8 35.1 + - + +
594A VAL* 4.6 0.7 - - + -
598A LEU* 4.0 26.5 - - + +
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Residues in contact with GLY 579 (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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182A TRP* 4.1 15.5 - - - -
575A PHE 2.9 13.8 + - - -
576A SER 3.6 5.8 - - - -
577A LEU 3.1 0.6 - - - -
578A ALA* 1.3 78.4 - - - +
580A ASN* 1.3 59.3 + - - +
582A ILE 3.2 20.7 - - - +
583A THR* 4.1 2.6 - - - +
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Residues in contact with ASN 580 (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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576A SER* 2.7 30.1 + - - +
577A LEU* 3.1 23.7 + - - +
579A GLY* 1.3 75.5 - - - +
581A ILE* 1.3 64.0 + - - +
583A THR* 3.2 16.7 - - - +
586A ARG* 4.3 3.5 + - - -
3B A 5.9 1.6 + - - -
4B G 5.3 5.5 - - - +
106E CYS* 3.9 20.3 - - - -
585E LYS* 3.0 34.1 + - + +
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Residues in contact with ILE 581 (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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577A LEU 3.3 11.7 + - - +
578A ALA* 3.0 10.6 + - - +
580A ASN* 1.3 78.1 - - - +
582A ILE* 1.3 58.5 + - + +
583A THR* 3.0 15.8 + - - +
586A ARG* 3.2 39.4 - - - +
589A ILE* 4.6 10.6 - - + +
594A VAL* 4.2 31.6 - - + -
597A LEU* 4.6 27.4 - - + -
598A LEU* 5.3 5.8 - - + -
106E CYS* 3.2 37.9 - - + -
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Residues in contact with ILE 582 (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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182A TRP* 3.9 27.8 - - + -
184A ASP* 3.9 29.7 - - + +
185A ASN* 4.7 2.8 + - - +
186A TYR* 4.1 16.7 - - + -
187A ILE* 5.4 4.0 - - + -
191A PHE* 4.4 10.1 - - + -
578A ALA* 2.8 21.4 + - + +
579A GLY* 3.2 12.5 - - - +
580A ASN 3.6 0.2 - - - -
581A ILE* 1.3 70.6 - - - +
583A THR* 1.3 62.2 + - - +
586A ARG 5.0 0.2 - - - -
587A ASN* 5.2 8.1 - - - +
589A ILE* 4.2 16.4 - - + -
594A VAL* 4.0 36.1 - - + -
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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