Contacts of the helix formed by residues 608 - 622 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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581L TRP* 3.8 3.9 - - - -
604L ASP* 4.4 7.2 - - - -
606L GLU 4.3 0.2 - - - -
607L PHE* 1.3 78.3 - - - +
609L LEU* 1.3 71.6 + - - +
610L SER* 2.9 27.4 + - - -
611L VAL* 3.7 13.3 - - - +
612L TYR* 3.6 18.4 + - - +
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Residues in contact with LEU 609 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581L TRP* 4.6 22.0 - - + +
604L ASP* 4.4 15.3 - - - +
608L SER* 1.3 82.1 - - - +
610L SER* 1.3 63.5 + - - +
612L TYR* 4.0 1.1 - - - -
613L GLN* 2.7 40.6 + - - +
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Residues in contact with SER 610 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608L SER* 2.9 15.6 + - - -
609L LEU* 1.3 76.2 - - - +
611L VAL* 1.3 72.7 + - - +
612L TYR 3.1 1.3 + - - -
613L GLN* 3.5 3.0 + - - +
614L LYS* 2.9 30.6 + - - +
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Residues in contact with VAL 611 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385L GLU* 5.9 1.3 - - - +
606L GLU 5.5 1.8 - - - +
607L PHE* 3.5 33.7 - - + -
608L SER* 3.7 21.9 + - - +
609L LEU 3.6 0.2 - - - -
610L SER* 1.3 87.1 + - - +
612L TYR* 1.3 61.6 + - - +
614L LYS* 3.6 8.4 - - + +
615L MET* 3.2 25.5 + - + +
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Residues in contact with TYR 612 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388L MET* 4.0 17.7 - - + -
391L VAL* 3.3 26.8 + - + +
392L ALA* 4.7 4.5 - - + -
581L TRP* 3.4 53.6 - + + -
582L TYR* 2.8 43.0 + + - -
607L PHE* 5.0 0.8 - - + -
608L SER 3.6 10.2 + - - +
609L LEU* 3.8 0.7 - - + +
610L SER 3.1 0.6 - - - -
611L VAL* 1.3 75.1 - - - +
613L GLN* 1.3 83.9 + - - +
614L LYS 3.0 3.6 - - - -
615L MET* 2.8 47.9 + - + +
616L LYS* 3.4 21.2 + - + +
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Residues in contact with GLN 613 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582L TYR* 5.1 1.4 + - - -
609L LEU* 2.7 44.1 + - - +
610L SER* 4.3 2.9 - - - +
612L TYR* 1.3 99.6 - - - +
614L LYS* 1.3 56.4 + - - +
615L MET 3.1 0.2 - - - -
616L LYS* 3.3 21.3 + - + +
617L PHE* 2.9 28.1 + - - +
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Residues in contact with LYS 614 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610L SER 2.9 19.4 + - - +
611L VAL* 3.6 12.6 - - + +
612L TYR 3.0 0.2 - - - -
613L GLN* 1.3 77.6 - - - +
615L MET* 1.3 59.8 + - + +
617L PHE* 3.3 39.5 - - + +
618L ASN* 2.8 23.1 + - - -
627L ASP* 4.0 26.8 + - - +
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Residues in contact with MET 615 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385L GLU 4.4 2.0 - - - +
388L MET* 3.8 20.2 - - + +
389L ALA* 3.7 14.4 - - - -
392L ALA* 4.1 9.9 - - + -
607L PHE* 4.2 16.8 - - + -
611L VAL* 3.2 12.3 - - + +
612L TYR* 2.8 46.9 + - + +
614L LYS* 1.3 76.7 - - + +
616L LYS* 1.3 61.7 + - - +
617L PHE 3.0 5.4 + - - -
618L ASN* 3.2 11.6 + - - +
619L VAL* 3.1 17.7 + - - +
625L VAL* 3.2 26.3 - - + +
626L LEU* 3.6 26.0 - - + -
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Residues in contact with LYS 616 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392L ALA* 3.5 19.1 - - + -
395L HIS* 2.9 47.2 + - - -
396L CYS* 4.1 18.8 - - - -
582L TYR* 3.3 13.1 + - - +
612L TYR* 3.8 32.1 - - + +
613L GLN* 3.3 21.4 + - + +
615L MET* 1.3 76.0 - - - +
617L PHE* 1.3 59.9 + - - +
619L VAL* 3.1 25.3 - - - +
620L ALA* 3.2 9.0 + - - +
14W ILE* 5.9 3.0 - - - +
15W PHE* 6.4 3.6 - - + -
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Residues in contact with PHE 617 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613L GLN 2.9 13.6 + - - +
614L LYS* 3.3 33.7 - - + +
616L LYS* 1.3 74.3 - - - +
618L ASN* 1.3 75.8 + - - +
619L VAL 3.0 1.8 - - - -
620L ALA* 2.9 25.1 + - + +
621L MET* 3.1 50.7 + - + +
623L ILE* 5.5 1.6 - - + -
43W GLY 5.1 0.4 - - - -
46W ILE* 5.9 3.4 - - + -
47W ALA* 5.0 15.5 - - + -
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Residues in contact with ASN 618 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614L LYS* 2.8 24.2 + - - +
615L MET* 3.2 5.3 + - - +
617L PHE* 1.3 88.0 - - - +
619L VAL* 1.3 56.5 + - - +
621L MET* 3.4 3.9 - - - +
622L GLY 2.8 24.9 + - - -
623L ILE* 3.0 40.3 + - + +
624L GLY 3.1 23.6 + - - +
625L VAL* 3.2 19.4 + - - -
627L ASP* 3.3 26.1 + - - +
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Residues in contact with VAL 619 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393L TRP* 4.3 10.3 - - + +
396L CYS* 3.6 31.9 - - + -
552L TYR* 3.1 42.1 - - + +
553L LEU* 4.1 8.5 - - + -
556L CYS* 4.0 15.7 - - + -
615L MET 3.1 17.3 - - - +
616L LYS* 3.1 16.6 - - - +
617L PHE 3.0 0.2 - - - -
618L ASN* 1.3 76.5 - - - +
620L ALA* 1.3 64.5 + - - +
621L MET 3.3 0.5 + - - -
622L GLY 3.5 1.4 + - - -
625L VAL* 3.5 22.9 - - + -
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Residues in contact with ALA 620 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396L CYS* 5.6 0.2 - - - -
552L TYR* 3.8 18.4 - - - +
616L LYS 3.2 6.8 + - - +
617L PHE* 2.9 13.9 + - + +
619L VAL* 1.3 80.2 - - - +
621L MET* 1.3 77.8 + - + +
15W PHE* 5.7 9.0 - - + -
39W GLU 4.4 6.3 - - - +
40W GLY* 5.1 3.5 - - - -
43W GLY* 4.1 19.8 - - - -
44W GLU* 4.9 1.6 - - - +
46W ILE* 6.5 0.7 - - + -
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Residues in contact with MET 621 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552L TYR* 4.8 2.9 - - - +
555L HIS* 5.5 1.9 - - - -
617L PHE* 3.1 55.2 + - + +
618L ASN* 3.4 12.6 - - - +
619L VAL 3.1 0.2 - - - -
620L ALA* 1.3 92.4 - - + +
622L GLY* 1.3 59.1 + - - +
623L ILE* 3.7 20.0 - - + -
43W GLY* 3.0 29.4 - - - +
44W GLU* 4.3 18.9 - - - +
47W ALA* 4.9 7.4 - - - -
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Residues in contact with GLY 622 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552L TYR* 3.9 17.3 - - - -
555L HIS* 2.8 33.7 - - - +
559L ARG* 2.8 29.5 + - - -
618L ASN 2.8 7.5 + - - -
619L VAL 3.5 2.0 + - - -
621L MET* 1.3 76.1 - - - +
623L ILE* 1.3 58.5 + - - +
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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