Contacts of the helix formed by residues 573 - 585 (chain A) in PDB entry 4EG8
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 GLY 573 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569A ALA* 2.6 22.3 + - - +
570A GLU 4.5 0.8 + - - -
571A GLU 3.7 1.0 - - - -
572A PHE* 1.3 74.4 - - - +
574A TYR* 1.3 59.8 + - - -
576A ALA 4.0 1.1 - - - -
577A LEU* 3.0 30.8 + - - +
765A ARG* 5.0 0.7 - - - -
808A GOL 3.5 25.8 - - - -
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Residues in contact with TYR 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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321A GLN* 2.7 51.5 + - + +
322A MET* 4.2 26.6 - - + +
323A ASP* 5.3 7.0 - - + +
566A VAL* 3.7 9.0 - - - +
569A ALA* 3.4 33.4 - - + -
570A GLU* 2.7 31.8 + - - +
573A GLY* 1.3 68.5 - - - -
575A ASP* 1.3 71.9 + - - +
576A ALA 3.3 0.2 + - - -
577A LEU* 3.3 2.9 + - - +
578A LYS* 3.1 33.5 + - - +
719A ARG* 6.3 1.1 - - + -
808A GOL 3.3 27.7 - - - +
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Residues in contact with ASP 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A TYR* 1.3 77.9 - - - +
576A ALA* 1.3 52.8 + - - +
578A LYS* 3.3 13.2 + - - +
579A TYR* 2.8 34.7 + - - +
716A ILE 4.3 0.4 - - - +
717A LEU* 3.1 34.7 - - + +
718A PRO* 3.6 16.3 - - - +
719A ARG* 2.8 37.8 + - - +
720A LYS* 2.8 22.4 + - + +
762A PHE* 5.2 0.2 - - + -
808A GOL 3.1 14.6 + - - +
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Residues in contact with ALA 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A PHE 3.7 15.5 - - - +
573A GLY 3.8 1.3 - - - +
574A TYR 3.2 0.8 - - - -
575A ASP* 1.3 74.6 - - - +
577A LEU* 1.3 61.1 + - - +
579A TYR* 3.4 3.8 + - - +
580A PHE* 2.8 30.1 + - - +
598A MET* 3.8 8.9 - - + +
602A LEU* 3.5 31.9 - - + -
606A LEU* 3.7 18.9 - - + +
762A PHE* 4.8 3.5 - - + -
808A GOL 3.3 7.5 + - - +
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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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322A MET* 4.8 8.7 - - + -
563A PHE* 4.4 17.7 - - + -
565A PRO* 3.2 42.4 - - + +
568A LYS* 4.1 16.4 - - + +
569A ALA* 3.7 16.2 - - + +
573A GLY 3.0 19.6 + - - +
574A TYR 3.3 4.0 + - - +
576A ALA* 1.3 73.3 - - - +
578A LYS* 1.3 61.9 + - + +
580A PHE* 3.4 1.8 + - + +
581A LEU* 3.0 43.7 + - + +
593A TYR* 4.4 11.9 - - + -
598A MET* 3.9 13.6 - - + +
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Residues in contact with LYS 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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264A LEU* 3.9 39.9 - - + +
267A ASP* 4.9 3.0 + - - -
271A ARG* 5.5 0.2 - - - +
322A MET* 2.9 48.7 + - + -
323A ASP* 3.0 22.4 + - - +
324A TYR* 4.5 5.0 - - - +
574A TYR* 3.1 24.5 + - - +
575A ASP* 3.5 16.0 + - - +
577A LEU* 1.3 74.1 - - + +
579A TYR* 1.3 65.3 + - - +
581A LEU* 3.2 3.5 + - + +
582A LEU* 3.0 31.7 + - + +
716A ILE 4.1 13.7 - - - +
718A PRO* 4.3 15.4 - - + +
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Residues in contact with TYR 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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575A ASP 2.8 21.1 + - - +
576A ALA* 3.4 7.2 - - - +
578A LYS* 1.3 71.8 - - - +
580A PHE* 1.3 64.1 + - + +
582A LEU* 3.1 3.3 + - - +
583A ARG* 2.8 55.7 + - + +
601A ARG* 4.4 10.1 - - + -
605A GLU* 2.6 42.1 + - + +
606A LEU* 3.9 28.3 - - + -
665A ILE* 3.5 15.3 - - + -
669A PHE* 3.5 38.1 - + - -
713A LEU* 5.5 0.4 - - + -
716A ILE* 3.8 23.4 - - + +
717A LEU* 3.9 12.8 - - + -
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Residues in contact with PHE 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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548A TRP* 4.5 6.3 - + - -
576A ALA 2.8 14.6 + - - +
577A LEU* 3.7 4.9 - - + +
578A LYS 3.3 0.2 - - - -
579A TYR* 1.3 81.3 - - + +
581A LEU* 1.3 65.4 + - + +
583A ARG* 4.5 2.2 - - - -
584A GLU* 2.9 56.1 + - + +
592A ASP 4.0 7.0 - - - -
593A TYR* 3.4 42.2 - + + -
597A ASN* 3.8 21.5 - - + -
598A MET* 3.5 53.8 - - - -
601A ARG* 3.7 20.2 - - + -
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Residues in contact with LEU 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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257A ILE* 3.8 22.7 - - + -
260A VAL* 4.9 10.1 - - + -
261A TYR* 3.6 26.3 - - + -
264A LEU* 4.5 16.2 - - + -
322A MET* 6.3 1.1 - - + -
548A TRP* 3.5 45.7 - - + +
563A PHE* 4.3 22.9 - - + -
577A LEU* 3.0 33.7 + - + +
578A LYS* 3.8 4.5 - - + +
580A PHE* 1.3 86.6 - - + +
582A LEU* 1.3 62.0 + - - +
583A ARG 3.7 0.2 + - - -
585A SER 4.2 7.6 + - - +
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Residues in contact with LEU 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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261A TYR* 4.6 6.3 - - + -
264A LEU* 3.9 22.7 - - + -
265A ILE* 4.1 25.4 - - + -
268A VAL* 3.7 26.0 - - + -
578A LYS* 3.0 22.2 + - + +
579A TYR 3.9 0.9 - - - +
581A LEU* 1.3 77.0 - - - +
583A ARG* 1.3 59.6 + - - +
585A SER 3.7 5.8 - - - +
587A PHE* 5.5 2.5 - - + -
661A ILE* 3.9 19.9 - - + +
662A GLN* 3.5 27.5 + - - +
665A ILE* 3.7 16.3 - - + +
716A ILE* 4.1 19.1 - - + +
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Residues in contact with ARG 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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579A TYR* 2.8 49.4 + - + +
580A PHE* 4.1 2.0 - - - +
582A LEU* 1.3 77.6 - - - +
584A GLU* 1.3 63.3 + - - +
585A SER 3.3 2.2 - - - -
601A ARG* 3.5 26.2 - - - +
605A GLU* 4.3 2.8 + - - -
662A GLN* 3.1 14.0 + - - +
665A ILE* 3.8 25.3 - - + +
666A ILE* 3.7 36.0 - - - +
669A PHE* 6.1 1.6 - - - +
673A ARG* 5.7 5.3 - - - +
802A GOL 3.3 47.7 + - - -
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Residues in contact with GLU 584 (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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548A TRP* 4.2 10.5 - - + -
580A PHE* 2.9 42.4 + - + +
583A ARG* 1.3 80.9 + - - +
585A SER* 1.3 58.4 + - - +
591A GLY* 5.3 0.2 - - - -
592A ASP* 3.8 21.6 + - - +
597A ASN* 2.8 28.5 + - - -
601A ARG* 2.7 39.2 + - - +
662A GLN* 3.6 4.9 - - - +
802A GOL 5.3 2.8 + - - -
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Residues in contact with SER 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A TYR* 4.3 9.7 + - - -
548A TRP* 4.0 14.4 - - - -
581A LEU 4.2 7.2 + - - +
582A LEU* 3.7 15.9 - - - +
584A GLU* 1.3 80.9 - - - +
586A GLY* 1.3 72.5 + - - +
587A PHE* 5.3 2.3 - - - -
589A ASP* 3.4 18.6 + - - +
591A GLY* 3.4 30.6 + - - -
662A GLN* 3.4 8.7 - - - +
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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