Contacts of the helix formed by residues 570 - 583 (chain A) in PDB entry 1L8A
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 ASN 570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A TYR* 2.8 29.5 + - - -
241A ALA* 4.7 6.1 - - - +
244A ILE* 4.8 4.8 - - - +
520A ALA* 4.5 1.7 - - - +
567A GLU* 3.5 18.9 + - - +
568A GLY 2.8 8.7 + - - -
569A ILE* 1.3 75.4 - - - +
571A GLU* 1.3 60.4 + - - +
572A LEU 3.6 0.3 + - - -
573A GLY* 2.7 25.7 + - - -
574A ALA* 2.9 27.8 + - - +
234B ASP* 3.5 22.3 + - + +
235B GLU* 3.4 5.4 + - - -
236B PRO* 3.1 22.0 - - - +
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Residues in contact with GLU 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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520A ALA* 4.4 12.5 - - + +
569A ILE* 5.3 0.7 - - - +
570A ASN* 1.3 73.0 + - - +
572A LEU* 1.3 58.5 + - - +
574A ALA* 4.3 0.2 - - - -
575A GLY* 2.8 26.2 + - - -
596A TYR* 3.4 24.9 + - - +
598A TYR* 4.9 5.9 - - + +
599A TYR* 5.6 1.2 + - - -
602A PHE* 3.6 36.7 - - + +
606A ARG* 4.6 7.0 - - + -
607A ILE* 3.9 14.5 - - + +
887A TPP 2.8 37.7 + - - +
235B GLU* 2.6 30.5 + - - +
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Residues in contact with LEU 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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196A LEU* 5.0 7.2 - - + -
199A ILE* 4.0 13.9 - - + -
237A GLU* 3.7 39.5 - - + +
570A ASN* 3.3 0.8 + - - -
571A GLU* 1.3 78.2 - - - +
573A GLY* 1.3 59.8 + - - +
575A GLY* 3.2 2.5 + - - -
576A CYS* 2.9 34.5 + - - -
606A ARG* 5.5 0.9 - - - +
607A ILE* 3.6 30.6 - - + +
610A LEU* 4.0 24.0 - - + -
235B GLU* 4.9 1.2 + - - -
236B PRO* 4.0 23.8 - - + -
237B GLU* 5.1 8.7 - - - +
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Residues in contact with GLY 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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199A ILE* 4.3 3.5 - - - +
203A TYR* 3.3 46.6 - - - -
567A GLU* 4.6 0.7 - - - -
570A ASN* 2.7 25.2 + - - -
572A LEU* 1.3 74.9 - - - +
574A ALA* 1.3 59.5 + - - +
576A CYS* 3.1 2.0 + - - +
577A SER* 3.0 18.2 + - - -
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Residues in contact with ALA 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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518A ILE* 4.0 13.4 - - + +
519A ILE 4.7 0.2 - - - +
520A ALA* 4.5 4.7 - - + -
567A GLU* 3.8 21.1 - - + +
570A ASN 2.9 16.5 + - - +
573A GLY* 1.3 71.9 - - - +
575A GLY* 1.3 61.4 + - - +
577A SER* 3.1 3.9 + - - +
578A TRP* 2.8 28.8 + - - +
596A TYR* 3.4 35.9 - - + +
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Residues in contact with GLY 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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571A GLU 2.8 16.2 + - - -
572A LEU 3.6 3.1 - - - -
574A ALA* 1.3 76.7 - - - +
576A CYS* 1.3 56.8 + - - +
578A TRP* 3.3 13.0 + - - +
579A LEU* 2.8 28.6 + - - +
596A TYR* 4.0 10.3 - - - -
607A ILE* 4.3 6.1 - - - -
610A LEU* 3.5 17.7 - - - +
623A LEU* 5.9 0.9 - - - -
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Residues in contact with CYS 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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199A ILE* 3.8 24.9 - - - +
200A GLY* 3.8 25.1 - - - +
203A TYR* 3.6 23.9 - - + +
572A LEU* 2.9 18.8 + - - +
573A GLY 3.4 9.2 - - - +
574A ALA 3.1 0.2 - - - -
575A GLY* 1.3 75.8 - - - +
577A SER* 1.3 58.2 + - - +
579A LEU* 3.5 7.7 + - - +
580A ALA* 3.0 27.0 + - - +
610A LEU* 3.8 20.4 - - - -
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Residues in contact with SER 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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203A TYR* 3.2 21.7 + - - +
206A LYS* 4.0 3.1 + - - +
207A PHE* 4.5 4.8 - - - +
518A ILE* 4.0 5.2 - - - -
565A LEU* 3.9 18.9 - - - +
567A GLU* 2.6 29.6 + - - -
573A GLY 3.0 8.0 + - - -
574A ALA* 3.1 8.5 + - - -
576A CYS* 1.3 72.8 - - - +
578A TRP* 1.3 67.8 + - - +
580A ALA* 3.2 6.3 + - - +
581A ALA* 2.9 24.6 + - - +
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Residues in contact with TRP 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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518A ILE* 3.4 15.0 - - + +
574A ALA 2.8 13.2 + - - +
575A GLY* 3.4 14.8 - - - +
577A SER* 1.3 77.9 - - - +
579A LEU* 1.3 68.1 + - + +
581A ALA 3.3 0.5 + - - -
582A ALA* 2.7 38.3 + - + +
594A PRO* 3.4 26.0 + - + +
596A TYR* 3.6 19.5 - - + -
610A LEU* 6.1 1.1 - - + -
611A CYS* 6.2 0.7 - - - -
614A ALA* 3.9 15.5 - - + -
619A ALA* 3.9 22.4 - - + -
621A GLY* 3.6 27.1 - - - -
622A PHE 2.8 31.4 + - - +
623A LEU* 3.5 31.0 - - + -
686A TYR* 3.7 31.4 - + + -
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Residues in contact with LEU 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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200A GLY* 5.9 5.2 - - - -
575A GLY 2.8 18.1 + - - +
576A CYS* 3.7 7.9 - - - +
577A SER 3.2 0.2 - - - -
578A TRP* 1.3 81.2 - - + +
580A ALA* 1.3 58.5 + - - +
582A ALA* 3.8 1.1 - - - -
583A THR* 2.7 52.6 + - + +
610A LEU* 4.0 26.9 - - + -
613A ALA* 5.2 2.5 - - + -
614A ALA* 3.8 34.8 - - + +
617A GLN* 3.5 27.6 - - + +
619A ALA* 3.9 5.6 - - + -
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Residues in contact with ALA 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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200A GLY 5.6 0.2 - - - +
203A TYR 4.0 2.0 - - - +
204A GLN* 3.9 32.8 + - + +
207A PHE* 3.7 30.7 - - + -
576A CYS 3.0 17.5 + - - +
577A SER 3.2 4.9 + - - +
579A LEU* 1.3 77.4 - - - +
581A ALA* 1.3 62.6 + - - +
583A THR* 3.5 5.7 + - - -
584A SER* 3.2 22.9 + - - -
617A GLN* 5.6 0.4 - - - +
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Residues in contact with ALA 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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207A PHE* 3.5 30.9 - - + -
516A VAL* 4.1 13.5 - - + -
577A SER 2.9 15.5 + - - +
578A TRP* 3.6 4.3 - - - +
580A ALA* 1.3 78.3 - - - +
582A ALA* 1.3 58.8 + - - +
583A THR 3.2 1.6 + - - -
584A SER* 3.3 14.4 + - - -
592A MET* 3.2 19.6 + - + +
594A PRO* 3.7 20.4 - - + -
678A TYR* 4.6 0.2 + - - -
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Residues in contact with ALA 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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578A TRP* 2.7 29.0 + - + +
579A LEU* 3.3 3.6 + - - +
581A ALA* 1.3 71.0 - - - +
583A THR* 1.3 58.3 + - - +
584A SER 3.6 0.2 - - - -
585A TYR* 3.3 13.0 - - - -
594A PRO* 3.6 11.4 - - + +
619A ALA* 3.8 14.8 - - + -
620A ARG 3.0 51.2 + - - +
621A GLY 4.3 1.1 - - - +
678A TYR* 4.1 2.5 - - - -
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Residues in contact with THR 583 (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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204A GLN* 4.8 2.3 + - - -
579A LEU* 2.7 27.6 + - + +
580A ALA* 3.5 6.7 + - - -
582A ALA* 1.3 82.9 - - - +
584A SER* 1.3 59.7 + - - +
585A TYR* 3.2 9.0 - - + -
586A SER* 3.2 8.0 + - - -
587A THR* 3.0 34.2 + - - -
617A GLN* 3.1 52.0 + - - +
618A GLN 4.2 1.3 - - - +
619A ALA* 3.7 13.7 - - - -
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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