Contacts of the helix formed by residues 573 - 585 (chain B) in PDB entry 4EGA
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569B ALA* 2.7 24.9 + - - -
570B GLU 4.7 0.2 - - - -
571B GLU 3.7 0.6 - - - -
572B PHE* 1.3 75.7 - - - +
574B TYR* 1.3 60.1 + - - -
575B ASP 3.6 1.3 - - - -
576B ALA* 3.9 4.9 - - - -
577B LEU* 2.9 29.6 + - - +
811B DMS 4.0 17.3 - - - -
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Residues in contact with TYR 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B GLN* 2.7 49.9 + - - -
322B MET* 4.3 24.2 - - + +
323B ASP* 5.6 5.4 - - + -
566B VAL* 3.6 10.3 - - + +
569B ALA* 3.3 32.8 - - + -
570B GLU* 3.0 37.5 + - - +
573B GLY* 1.3 68.5 - - - -
575B ASP* 1.3 68.0 + - - +
577B LEU* 3.1 3.6 + - - +
578B LYS* 2.9 37.5 + - - +
811B DMS 3.5 31.6 - - + -
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Residues in contact with ASP 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ASP* 5.0 0.2 - - - +
574B TYR* 1.3 76.0 - - - +
576B ALA* 1.3 64.1 + - - +
578B LYS* 3.3 12.8 + - - +
579B TYR 2.9 20.3 + - - -
716B ILE 4.7 0.9 - - - -
717B LEU* 3.1 34.2 - - + +
718B PRO* 3.9 7.2 - - - +
719B ARG* 2.8 28.1 + - - +
720B LYS* 2.7 47.4 + - + +
811B DMS 3.5 14.4 - - + +
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Residues in contact with ALA 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B PHE 3.4 26.2 - - - +
573B GLY* 3.6 5.1 - - - +
575B ASP* 1.3 80.3 - - - +
577B LEU* 1.3 61.7 + - - +
579B TYR* 3.4 5.0 + - - +
580B PHE* 3.1 21.8 + - - +
598B MET* 3.9 15.1 - - + +
602B LEU* 4.5 9.4 - - + -
606B LEU* 3.9 23.7 - - + +
717B LEU* 4.4 0.2 - - - +
720B LYS* 5.8 1.9 - - - +
762B PHE* 5.1 5.5 - - + -
811B DMS 5.5 0.6 - - - -
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Residues in contact with LEU 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B MET* 4.8 10.3 - - + -
563B PHE* 4.4 8.5 - - + -
565B PRO* 3.2 42.2 - - + +
568B LYS* 4.2 16.6 - - + -
569B ALA* 3.8 14.4 - - + +
573B GLY 2.9 19.0 + - - +
574B TYR* 3.1 6.0 + - - +
576B ALA* 1.3 75.8 - - - +
578B LYS* 1.3 64.5 + - + +
580B PHE* 3.1 4.3 + - + +
581B LEU* 3.0 36.8 + - + +
593B TYR* 4.2 20.2 - - + -
598B MET* 4.1 13.9 - - + +
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Residues in contact with LYS 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B LEU* 3.8 32.8 - - + -
267B ASP* 4.8 2.0 + - - -
271B ARG* 4.7 1.0 - - - +
322B MET* 2.9 43.5 + - + -
323B ASP* 2.9 24.7 + - - +
324B TYR* 4.1 16.3 - - - -
574B TYR* 2.9 27.1 + - - +
575B ASP* 3.7 12.4 + - - +
577B LEU* 1.3 74.2 - - - +
579B TYR* 1.3 65.5 + - - +
580B PHE 3.2 0.2 + - - -
581B LEU* 3.3 2.1 + - - +
582B LEU* 3.1 30.6 + - + +
716B ILE* 4.0 15.7 - - - +
718B PRO* 4.4 15.5 - - + +
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Residues in contact with TYR 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575B ASP 2.9 12.5 + - - +
576B ALA 3.4 9.4 - - - +
578B LYS* 1.3 75.8 - - - +
580B PHE* 1.3 62.8 + - + +
582B LEU* 3.8 1.0 - - - +
583B ARG* 2.8 53.5 + - + +
601B ARG* 4.3 11.9 - - + -
605B GLU* 2.6 41.6 + - + +
606B LEU* 3.7 33.0 - - + -
665B ILE* 3.8 16.3 - - + +
669B PHE* 3.6 31.4 - + - -
713B LEU* 5.1 1.1 - - + -
716B ILE* 3.9 24.0 - - + +
717B LEU* 3.7 15.9 - - + -
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Residues in contact with PHE 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B TRP* 4.8 3.1 - + - -
576B ALA 3.1 4.9 + - - +
577B LEU* 3.1 9.7 + - + +
579B TYR* 1.3 82.3 - - + +
581B LEU* 1.3 67.2 + - + +
583B ARG* 4.7 1.8 - - - -
584B GLU* 2.7 59.7 + - + +
593B TYR* 3.2 50.0 - + + -
597B ASN* 3.6 20.6 - - + -
598B MET* 3.5 52.5 - - - -
601B ARG* 3.8 27.6 - - + -
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Residues in contact with LEU 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B ILE* 3.9 23.8 - - + -
260B VAL* 5.1 6.5 - - + -
261B TYR* 3.9 22.0 - - + -
264B LEU* 4.1 23.6 - - + -
322B MET* 6.1 1.6 - - + -
548B TRP* 3.5 41.1 - - + -
563B PHE* 4.4 21.8 - - + -
577B LEU* 3.0 30.1 + - + +
578B LYS* 3.9 3.6 - - - +
580B PHE* 1.3 91.3 - - + +
582B LEU* 1.3 61.1 + - - +
585B SER 4.0 10.4 + - - +
593B TYR* 4.6 2.0 - - + -
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Residues in contact with LEU 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B TYR* 4.4 9.9 - - + +
264B LEU* 4.1 22.0 - - + -
265B ILE* 4.1 25.6 - - + -
268B VAL* 3.5 28.7 - - + -
578B LYS* 3.1 18.8 + - + +
579B TYR 4.6 0.2 - - - -
581B LEU* 1.3 76.5 - - - +
583B ARG* 1.3 63.3 + - - +
585B SER 3.6 12.6 - - - +
661B ILE* 4.2 19.0 - - + +
662B GLN* 3.7 18.9 + - - +
665B ILE* 3.8 15.5 - - + -
716B ILE* 4.1 21.5 - - + -
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Residues in contact with ARG 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579B TYR* 2.8 43.9 + - + +
580B PHE* 4.1 1.3 - - - +
582B LEU* 1.3 78.7 - - - +
584B GLU* 1.3 63.4 + - - +
601B ARG* 3.7 23.9 - - - +
605B GLU* 4.0 12.8 + - - +
662B GLN* 3.0 21.2 + - - +
665B ILE* 3.8 28.6 - - + +
666B ILE* 3.7 35.0 - - - +
669B PHE* 6.1 2.4 - - - +
673B ARG* 5.3 7.5 - - - +
803B GOL 3.1 44.7 + - - -
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Residues in contact with GLU 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B TRP* 4.2 13.2 - - + -
580B PHE* 2.7 44.6 + - + +
582B LEU 3.5 0.2 - - - -
583B ARG* 1.3 76.0 - - - +
585B SER* 1.3 59.5 + - - +
592B ASP* 3.9 21.7 + - - +
597B ASN* 3.1 23.8 + - - -
601B ARG* 2.6 43.6 + - - +
662B GLN* 3.3 7.5 + - - -
803B GOL 4.7 7.7 + - - -
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Residues in contact with SER 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B TYR* 3.9 12.3 + - - -
548B TRP* 4.2 10.1 - - - -
581B LEU 4.0 4.6 + - - +
582B LEU 3.6 14.0 - - - +
584B GLU* 1.3 80.6 - - - +
586B GLY* 1.3 62.7 + - - +
589B ASP* 2.9 39.4 + - - +
591B GLY* 3.3 30.9 + - - -
662B GLN* 3.7 6.0 - - - +
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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