Contacts of the helix formed by residues 608 - 622 (chain D) in PDB entry 4E2I
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 608 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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581D TRP* 3.8 4.6 - - - -
604D ASP* 4.5 6.7 - - - -
606D GLU 4.3 0.4 + - - -
607D PHE* 1.3 77.8 - - - +
609D LEU* 1.3 72.1 + - - +
610D SER* 2.9 27.0 + - - -
611D VAL* 3.7 13.6 - - - +
612D TYR* 3.6 18.2 + - - +
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Residues in contact with LEU 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581D TRP* 4.6 22.7 - - + +
604D ASP* 4.4 15.7 - - - +
608D SER* 1.3 82.1 - - - +
610D SER* 1.3 63.4 + - - +
612D TYR* 4.0 1.1 - - - -
613D GLN* 2.7 41.2 + - - +
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Residues in contact with SER 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608D SER* 2.9 16.3 + - - -
609D LEU* 1.3 75.2 - - - +
611D VAL* 1.3 73.4 + - - +
612D TYR 3.1 1.3 - - - -
613D GLN* 3.5 3.4 + - - +
614D LYS* 2.9 31.6 + - - +
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Residues in contact with VAL 611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D GLU* 5.9 1.3 - - - +
606D GLU 5.5 1.8 - - - +
607D PHE* 3.5 33.4 - - + -
608D SER* 3.7 22.1 + - - +
610D SER* 1.3 86.5 + - - +
612D TYR* 1.3 61.9 + - - +
614D LYS* 3.6 8.7 - - + +
615D MET* 3.2 24.4 + - + +
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Residues in contact with TYR 612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388D MET* 4.0 17.9 - - + -
391D VAL* 3.3 27.1 + - + +
392D ALA* 4.7 4.5 - - + -
581D TRP* 3.4 53.2 - + + -
582D TYR* 2.8 43.0 + + - -
607D PHE* 5.0 1.5 - - + -
608D SER 3.6 9.8 + - - +
609D LEU* 3.9 1.3 - - + +
610D SER 3.1 0.2 - - - -
611D VAL* 1.3 75.5 - - - +
613D GLN* 1.3 85.7 + - - +
614D LYS 3.0 4.0 - - - -
615D MET* 2.8 47.1 + - + +
616D LYS* 3.4 20.7 + - + +
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Residues in contact with GLN 613 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582D TYR* 5.1 1.6 + - - -
609D LEU* 2.7 43.1 + - - +
610D SER* 4.3 2.0 - - - +
612D TYR* 1.3 98.1 - - - +
614D LYS* 1.3 56.3 + - - +
615D MET 3.1 0.2 - - - -
616D LYS* 3.3 20.2 + - + +
617D PHE* 2.9 28.6 + - - +
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Residues in contact with LYS 614 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610D SER 2.9 19.6 + - - +
611D VAL* 3.6 13.2 - - + +
612D TYR 3.0 0.2 - - - -
613D GLN* 1.3 77.7 - - - +
615D MET* 1.3 58.3 + - + +
617D PHE* 3.3 39.7 - - + +
618D ASN* 2.8 23.6 + - - -
627D ASP* 4.0 27.7 + - - +
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Residues in contact with MET 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D GLU 4.4 2.2 - - - +
388D MET* 3.8 20.9 - - + +
389D ALA* 3.7 14.4 - - - -
392D ALA* 4.1 10.5 - - + -
607D PHE* 4.2 16.4 - - + -
611D VAL* 3.2 12.8 - - + +
612D TYR* 2.8 46.2 + - + +
614D LYS* 1.3 76.3 - - + +
616D LYS* 1.3 61.2 + - - +
617D PHE 3.0 5.0 + - - -
618D ASN* 3.2 11.6 + - - +
619D VAL* 3.1 17.8 + - - +
625D VAL* 3.2 26.3 - - + +
626D LEU* 3.6 26.2 - - + -
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Residues in contact with LYS 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144 ILE 4.5 7.2 + - - -
154 PHE* 4.7 6.3 - - + +
392D ALA* 3.5 20.0 - - + -
395D HIS* 2.9 46.5 + - - -
396D CYS* 4.1 18.4 - - - -
582D TYR* 3.3 13.7 + - - -
612D TYR* 3.8 32.7 - - + +
613D GLN* 3.3 21.1 + - + +
615D MET* 1.3 76.3 - - - +
617D PHE* 1.3 62.3 + - - +
619D VAL* 3.1 25.0 - - - +
620D ALA* 3.2 8.3 + - - +
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Residues in contact with PHE 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464 ILE* 5.4 4.7 - - + -
504 THR* 4.0 27.6 - - + -
613D GLN 2.9 13.4 + - - +
614D LYS* 3.3 34.3 - - + +
616D LYS* 1.3 74.1 - - - +
618D ASN* 1.3 75.2 + - - +
619D VAL 3.0 1.3 - - - -
620D ALA* 2.9 24.6 + - + +
621D MET* 3.1 50.4 + - + +
623D ILE* 5.5 1.6 - - + -
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Residues in contact with ASN 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614D LYS* 2.8 24.2 + - - +
615D MET* 3.2 5.7 + - - +
617D PHE* 1.3 87.0 - - - +
619D VAL* 1.3 55.8 + - - +
621D MET* 3.4 3.7 - - - +
622D GLY 2.8 25.8 + - - -
623D ILE* 3.0 40.3 + - + +
624D GLY 3.1 23.8 + - - +
625D VAL 3.2 19.0 + - - -
627D ASP* 3.3 25.7 + - - +
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Residues in contact with VAL 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D TRP* 4.3 10.1 - - + +
396D CYS* 3.6 31.6 - - + -
552D TYR* 3.1 41.5 - - + +
553D LEU* 4.1 8.7 - - + -
556D CYS* 4.0 17.0 - - + -
615D MET 3.1 18.2 - - - +
616D LYS* 3.1 17.3 - - - +
617D PHE 3.0 0.4 - - - -
618D ASN* 1.3 77.3 - - - +
620D ALA* 1.3 64.6 + - - +
621D MET 3.3 0.5 + - - -
622D GLY 3.5 1.7 + - - -
625D VAL* 3.5 22.2 - - + -
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Residues in contact with ALA 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154 PHE* 3.5 41.7 - - + -
434 GLY* 5.5 7.4 - - - +
464 ILE* 4.5 12.6 - - + +
552D TYR* 3.8 10.2 - - - +
616D LYS 3.2 4.3 + - - +
617D PHE* 2.9 13.6 + - + +
619D VAL* 1.3 80.1 - - - +
621D MET* 1.3 78.6 + - + +
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Residues in contact with MET 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464 ILE* 4.2 22.9 - - + +
474 ALA* 5.6 6.1 - - - -
504 THR* 4.8 5.8 - - - -
552D TYR* 4.8 3.0 - - - +
555D HIS* 5.5 1.7 - - - -
617D PHE* 3.1 56.3 + - + +
618D ASN* 3.4 11.9 - - - +
620D ALA* 1.3 94.8 - - + +
622D GLY* 1.3 58.6 + - - +
623D ILE* 3.7 20.9 - - + -
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Residues in contact with GLY 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552D TYR* 3.9 17.3 - - - -
555D HIS* 2.8 33.1 - - - +
556D CYS 4.0 0.4 - - - -
559D ARG* 2.8 29.8 + - - -
618D ASN 2.8 8.1 + - - -
619D VAL 3.5 1.2 + - - -
621D MET* 1.3 75.8 - - - +
623D ILE* 1.3 58.1 + - - +
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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