Contacts of the helix formed by residues 608 - 622 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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581I TRP* 3.8 4.8 - - - -
604I ASP* 4.4 6.7 - - - -
606I GLU 4.4 0.2 + - - -
607I PHE* 1.3 77.6 - - - +
609I LEU* 1.3 71.3 + - - +
610I SER* 2.9 27.4 + - - -
611I VAL* 3.7 12.4 - - - +
612I TYR* 3.6 18.4 + - - +
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Residues in contact with LEU 609 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581I TRP* 4.6 21.8 - - + +
604I ASP* 4.4 15.3 - - - +
608I SER* 1.3 81.0 - - - +
610I SER* 1.3 63.2 + - - +
612I TYR* 4.0 1.3 - - - -
613I GLN* 2.7 41.8 + - - +
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Residues in contact with SER 610 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608I SER* 2.9 16.5 + - - -
609I LEU* 1.3 76.2 - - - +
611I VAL* 1.3 73.0 + - - +
612I TYR 3.1 1.6 - - - -
613I GLN* 3.5 2.6 + - - +
614I LYS* 3.0 31.1 + - - +
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Residues in contact with VAL 611 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385I GLU* 5.9 1.1 - - - +
606I GLU 5.5 2.0 - - - +
607I PHE* 3.5 33.7 - - + -
608I SER* 3.7 22.8 + - - +
609I LEU 3.6 0.2 - - - -
610I SER* 1.3 87.3 + - - +
612I TYR* 1.3 60.3 - - - +
614I LYS* 3.6 9.2 - - + +
615I MET* 3.2 24.5 + - + +
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Residues in contact with TYR 612 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388I MET* 4.0 17.7 - - + -
391I VAL* 3.3 26.7 + - + +
392I ALA* 4.4 4.7 + - + -
581I TRP* 3.4 53.6 - + + -
582I TYR* 2.8 42.8 + + - -
607I PHE* 5.0 0.6 - - - -
608I SER 3.6 10.2 + - - +
609I LEU* 3.9 0.9 - - + +
610I SER 3.1 0.8 - - - -
611I VAL* 1.3 74.7 - - - +
613I GLN* 1.3 85.1 + - - +
614I LYS 3.0 3.8 - - - -
615I MET* 2.8 47.4 + - + +
616I LYS* 3.4 21.2 + - + +
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Residues in contact with GLN 613 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159 PHE 5.9 2.9 - - - +
582I TYR* 5.1 0.9 + - - -
609I LEU* 2.7 43.8 + - - +
610I SER* 4.3 1.8 - - - +
612I TYR* 1.3 98.4 - - - +
614I LYS* 1.3 56.5 + - - +
615I MET 3.1 0.2 - - - -
616I LYS* 3.3 21.0 + - + +
617I PHE* 2.9 28.6 + - - +
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Residues in contact with LYS 614 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509 THR* 5.9 4.0 - - - -
610I SER 3.0 19.2 + - - +
611I VAL* 3.6 13.2 - - + +
612I TYR 3.0 0.6 - - - -
613I GLN* 1.3 78.5 - - - +
615I MET* 1.3 60.0 + - + +
617I PHE* 3.3 39.6 - - + +
618I ASN* 2.8 22.8 + - - -
627I ASP* 4.0 28.4 + - - +
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Residues in contact with MET 615 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385I GLU 4.4 2.5 - - - +
388I MET* 3.8 20.9 - - + +
389I ALA* 3.7 14.6 - - - -
392I ALA* 4.1 10.5 - - + -
607I PHE* 4.2 16.6 - - + -
611I VAL* 3.2 12.8 - - + +
612I TYR* 2.8 45.6 + - + +
614I LYS* 1.3 77.4 - - + +
616I LYS* 1.3 61.9 + - - +
617I PHE 3.0 5.0 + - - -
618I ASN* 3.2 11.3 + - - +
619I VAL* 3.1 17.8 + - - +
625I VAL* 3.2 26.3 - - + +
626I LEU* 3.6 26.2 - - + -
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Residues in contact with LYS 616 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149 ILE* 4.0 13.8 + - - -
159 PHE* 3.7 20.5 - - + +
392I ALA* 3.5 19.3 - - + +
395I HIS* 2.9 45.7 + - - -
396I CYS* 4.1 15.0 - - - -
582I TYR* 3.3 13.5 + - - +
612I TYR* 3.8 32.5 - - + +
613I GLN* 3.3 20.7 + - + +
615I MET* 1.3 75.7 - - - +
617I PHE* 1.3 62.7 + - - +
619I VAL* 3.1 24.6 - - - +
620I ALA 3.2 5.2 + - - -
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Residues in contact with PHE 617 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159 PHE* 5.6 2.0 - - - -
469 ILE* 3.2 38.4 - - + -
479 ALA* 4.3 2.0 - - + -
509 THR* 3.0 31.4 - - + -
613I GLN 2.9 14.4 + - - +
614I LYS* 3.3 33.9 - - + +
616I LYS* 1.3 73.5 - - - +
618I ASN* 1.3 76.4 + - - +
619I VAL 3.0 1.8 - - - -
620I ALA* 2.9 23.9 + - - +
621I MET* 3.1 43.4 + - + +
623I ILE* 5.5 1.3 - - + -
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Residues in contact with ASN 618 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614I LYS* 2.8 24.3 + - - +
615I MET 3.2 5.0 + - - +
617I PHE* 1.3 88.1 - - - +
619I VAL* 1.3 56.7 + - - +
621I MET* 3.2 3.9 + - - +
622I GLY 2.8 25.1 + - - -
623I ILE* 3.0 40.0 + - + +
624I GLY 3.1 24.0 + - - +
625I VAL 3.2 18.8 + - - -
627I ASP* 3.3 25.5 + - - +
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Residues in contact with VAL 619 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393I TRP* 4.3 9.9 - - + +
396I CYS* 3.6 31.9 - - + -
552I TYR* 3.1 41.1 - - + +
553I LEU* 4.1 9.0 - - + -
556I CYS* 4.0 15.3 - - + -
615I MET 3.1 17.9 - - - +
616I LYS* 3.1 16.8 - - - +
617I PHE 3.0 0.2 - - - -
618I ASN* 1.3 77.3 - - - +
620I ALA* 1.3 65.5 + - - +
621I MET 3.3 0.3 + - - -
622I GLY 3.5 1.6 + - - -
625I VAL* 3.5 22.9 - - + -
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Residues in contact with ALA 620 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159 PHE* 3.4 32.7 - - + -
429 VAL 5.4 0.2 - - - -
439 GLY* 2.9 23.6 - - - -
469 ILE* 3.6 24.2 - - + -
552I TYR* 3.8 14.3 - - - +
616I LYS 3.2 2.3 + - - +
617I PHE* 2.9 12.7 + - - +
619I VAL* 1.3 80.2 - - - +
621I MET* 1.3 67.1 + - + +
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Residues in contact with MET 621 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439 GLY* 3.1 24.1 - - - +
449 GLU* 4.6 10.6 - - - +
469 ILE* 3.5 19.7 - - + -
479 ALA* 3.4 29.6 - - - -
552I TYR* 4.8 2.3 - - - +
555I HIS* 5.6 2.1 - - - -
617I PHE* 3.1 51.3 + - + +
618I ASN* 3.4 13.0 - - - +
619I VAL 3.2 0.2 - - - -
620I ALA* 1.3 86.5 - - + +
622I GLY* 1.3 59.3 + - - +
623I ILE* 3.7 20.9 - - + +
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Residues in contact with GLY 622 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552I TYR* 3.9 16.6 - - - -
555I HIS* 2.8 32.8 - - - +
556I CYS* 4.0 0.4 - - - -
559I ARG* 2.8 23.4 + - - -
618I ASN 2.8 7.2 + - - -
619I VAL 3.5 1.6 + - - -
621I MET* 1.3 75.5 - - - +
623I ILE* 1.3 64.1 + - - +
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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