Contacts of the helix formed by residues 608 - 622 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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581K TRP* 3.8 4.7 - - - -
604K ASP* 4.4 7.0 - - - -
606K GLU 4.3 0.4 + - - -
607K PHE* 1.3 77.6 - - - +
609K LEU* 1.3 70.5 + - - +
610K SER* 2.9 28.0 + - - -
611K VAL* 3.7 13.5 - - - +
612K TYR* 3.6 18.4 + - - +
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Residues in contact with LEU 609 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581K TRP* 4.6 22.2 - - + +
604K ASP* 4.4 15.7 - - - +
608K SER* 1.3 81.8 - - - +
610K SER* 1.3 64.5 + - - +
612K TYR* 4.0 0.7 - - - -
613K GLN* 2.7 41.0 + - - +
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Residues in contact with SER 610 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608K SER* 2.9 15.0 + - - -
609K LEU* 1.3 75.8 - - - +
611K VAL* 1.3 72.8 + - - +
612K TYR 3.1 1.3 - - - -
613K GLN* 3.5 2.8 + - - +
614K LYS* 3.0 31.3 + - - +
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Residues in contact with VAL 611 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385K GLU* 5.9 0.9 - - - +
606K GLU 5.5 2.0 - - - +
607K PHE* 3.5 34.5 - - + -
608K SER* 3.7 22.4 + - - +
609K LEU 3.6 0.2 - - - -
610K SER* 1.3 85.9 + - - +
612K TYR* 1.3 61.5 + - - +
614K LYS* 3.6 8.7 - - + +
615K MET* 3.2 25.9 + - + +
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Residues in contact with TYR 612 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388K MET* 4.0 18.4 - - + -
391K VAL* 3.3 27.2 + - + +
392K ALA* 4.4 4.4 + - + -
581K TRP* 3.4 54.1 - + + -
582K TYR* 2.8 43.5 + + - -
607K PHE* 5.0 0.8 - - - -
608K SER 3.6 9.6 + - - +
609K LEU* 3.9 1.1 - - + +
610K SER 3.1 0.8 - - - -
611K VAL* 1.3 75.3 - - - +
613K GLN* 1.3 85.7 + - - +
614K LYS 3.0 3.4 - - - -
615K MET* 2.9 47.5 + - + +
616K LYS* 3.4 21.8 + - + +
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Residues in contact with GLN 613 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582K TYR* 5.1 1.0 + - - -
609K LEU* 2.7 43.8 + - - +
610K SER* 4.3 2.2 - - - +
612K TYR* 1.3 98.3 - - - +
614K LYS* 1.3 57.0 + - - +
615K MET 3.1 0.2 - - - -
616K LYS* 3.3 21.3 + - + +
617K PHE* 2.9 28.1 + - - +
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Residues in contact with LYS 614 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610K SER 3.0 20.0 + - - +
611K VAL* 3.6 12.8 - - + +
612K TYR 3.0 0.2 - - - -
613K GLN* 1.3 77.1 - - - +
615K MET* 1.3 58.3 + - + +
617K PHE* 3.3 41.0 - - + +
618K ASN* 2.8 23.6 + - - -
627K ASP* 4.0 27.3 + - - +
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Residues in contact with MET 615 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385K GLU 4.4 2.5 - - - +
388K MET* 3.8 20.9 - - + +
389K ALA* 3.7 14.1 - - - -
392K ALA* 4.1 9.6 - - + -
607K PHE* 4.2 15.9 - - + -
611K VAL* 3.2 13.5 - - + +
612K TYR* 2.9 46.9 + - + +
614K LYS* 1.3 77.0 - - + +
616K LYS* 1.3 60.6 + - - +
617K PHE 3.0 5.5 + - - -
618K ASN* 3.2 11.6 + - - +
619K VAL* 3.1 18.2 + - - +
625K VAL* 3.2 26.5 - - + +
626K LEU* 3.6 26.0 - - + -
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Residues in contact with LYS 616 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392K ALA* 3.5 20.0 - - + -
395K HIS* 2.9 44.7 + - - -
396K CYS* 4.1 19.1 - - - -
582K TYR* 3.3 13.3 + - - +
612K TYR* 3.8 31.6 - - + +
613K GLN* 3.3 20.6 + - + +
615K MET* 1.3 76.0 - - - +
617K PHE* 1.3 62.9 + - - +
619K VAL* 3.2 25.2 - - - +
620K ALA* 3.2 8.8 + - - +
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Residues in contact with PHE 617 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613K GLN 2.9 14.5 + - - +
614K LYS* 3.3 34.3 - - + +
616K LYS* 1.3 74.6 - - - +
618K ASN* 1.3 76.4 + - - +
619K VAL 3.0 1.1 - - - -
620K ALA* 2.9 24.7 + - + +
621K MET* 3.1 51.2 + - + +
623K ILE* 5.5 1.1 - - + -
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Residues in contact with ASN 618 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614K LYS* 2.8 24.5 + - - +
615K MET 3.2 5.7 + - - +
617K PHE* 1.3 87.0 - - - +
619K VAL* 1.3 57.5 + - - +
621K MET* 3.4 3.3 - - - +
622K GLY 2.8 25.8 + - - -
623K ILE* 3.0 41.2 + - + +
624K GLY 3.1 23.6 + - - +
625K VAL 3.2 18.8 + - - -
627K ASP* 3.3 24.7 + - - +
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Residues in contact with VAL 619 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393K TRP* 4.3 10.3 - - + +
396K CYS* 3.6 31.9 - - + -
552K TYR* 3.1 41.5 - - + +
553K LEU* 4.1 8.5 - - + -
556K CYS* 4.0 16.8 - - + -
615K MET 3.1 17.9 - - - +
616K LYS* 3.2 16.4 - - - +
617K PHE 3.0 0.4 - - - -
618K ASN* 1.3 80.4 - - - +
620K ALA* 1.3 62.6 + - - +
621K MET 3.3 0.3 + - - -
622K GLY 3.5 1.2 + - - -
625K VAL* 3.5 22.9 - - + -
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Residues in contact with ALA 620 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396K CYS* 5.6 0.6 - - - -
552K TYR* 3.8 19.0 - - - +
616K LYS 3.2 7.0 + - - +
617K PHE* 2.9 13.8 + - + +
619K VAL* 1.3 80.1 - - - +
621K MET* 1.3 77.4 + - + +
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Residues in contact with MET 621 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552K TYR* 4.8 2.8 - - - +
555K HIS* 5.6 1.7 - - - -
617K PHE* 3.1 55.4 + - + +
618K ASN* 3.4 13.5 - - - +
619K VAL 3.2 0.2 - - - -
620K ALA* 1.3 94.1 - - + +
622K GLY* 1.3 58.6 + - - +
623K ILE* 3.7 20.0 - - + -
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Residues in contact with GLY 622 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552K TYR* 3.9 16.4 - - - -
555K HIS* 2.8 33.7 - - - +
556K CYS 4.0 0.2 - - - -
559K ARG* 2.8 23.4 + - - -
618K ASN 2.8 7.3 + - - -
619K VAL 3.5 1.6 + - - -
621K MET* 1.3 76.8 - - - +
623K ILE* 1.3 64.8 + - - +
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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