Contacts of the helix formed by residues 608 - 622 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581G TRP* 3.8 4.1 - - - -
604G ASP* 4.4 6.5 + - - -
607G PHE* 1.3 79.4 - - - +
609G LEU* 1.3 70.5 + - - +
610G SER* 2.9 27.7 + - - -
611G VAL* 3.7 12.2 - - - +
612G TYR* 3.6 17.8 + - - +
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Residues in contact with LEU 609 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581G TRP* 4.5 22.7 - - + +
604G ASP* 4.4 15.5 - - - +
608G SER* 1.3 81.4 - - - +
610G SER* 1.3 63.2 + - - +
612G TYR* 4.0 1.1 - - - -
613G GLN* 2.7 41.9 + - - +
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Residues in contact with SER 610 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608G SER* 2.9 15.9 + - - -
609G LEU* 1.3 76.4 - - - +
611G VAL* 1.3 73.4 + - - +
612G TYR 3.1 1.3 - - - -
613G GLN* 3.5 2.9 + - - +
614G LYS* 3.0 31.2 + - - +
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Residues in contact with VAL 611 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385G GLU* 5.9 1.1 - - - +
606G GLU 5.5 1.6 - - - +
607G PHE* 3.5 35.0 - - + -
608G SER* 3.7 21.9 + - - +
609G LEU 3.6 0.2 - - - -
610G SER* 1.3 87.4 + - - +
612G TYR* 1.3 61.1 + - - +
614G LYS* 3.6 9.2 - - + +
615G MET* 3.2 24.7 + - + +
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Residues in contact with TYR 612 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388G MET* 4.0 18.2 - - + -
391G VAL* 3.3 26.8 + - + +
392G ALA* 4.7 4.5 - - + -
581G TRP* 3.4 52.5 - + + -
582G TYR* 2.8 43.9 + + - -
607G PHE* 5.0 1.5 - - + -
608G SER 3.6 10.0 + - - +
609G LEU* 3.9 0.9 - - + +
610G SER 3.1 0.2 - - - -
611G VAL* 1.3 74.7 - - - +
613G GLN* 1.3 84.4 + - - +
614G LYS 3.0 3.6 - - - -
615G MET* 2.9 46.9 + - + +
616G LYS* 3.4 21.1 + - + +
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Residues in contact with GLN 613 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582G TYR* 5.1 1.2 + - - -
609G LEU* 2.7 43.7 + - - +
610G SER* 4.3 2.2 - - - +
612G TYR* 1.3 98.8 - - - +
614G LYS* 1.3 56.6 + - - +
616G LYS* 3.3 21.0 + - + +
617G PHE* 2.9 28.5 + - - +
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Residues in contact with LYS 614 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507 THR* 6.3 2.5 - - - -
610G SER 3.0 19.6 + - - +
611G VAL* 3.6 12.6 - - + +
612G TYR 3.0 0.4 - - - -
613G GLN* 1.3 79.2 - - - +
615G MET* 1.3 58.1 + - + +
617G PHE* 3.2 40.9 - - + +
618G ASN* 2.8 22.7 + - - -
627G ASP* 4.0 27.1 + - - +
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Residues in contact with MET 615 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385G GLU 4.4 2.2 - - - +
388G MET* 3.8 20.9 - - + +
389G ALA* 3.7 14.6 - - - -
392G ALA* 4.1 10.1 - - + -
607G PHE* 4.2 16.2 - - + -
611G VAL* 3.2 12.8 - - + +
612G TYR* 2.9 46.5 + - + +
614G LYS* 1.3 76.4 - - + +
616G LYS* 1.3 61.3 + - - +
617G PHE 3.0 5.6 + - - -
618G ASN* 3.2 11.6 + - - +
619G VAL* 3.1 17.9 + - - +
625G VAL* 3.2 26.7 - - + +
626G LEU* 3.6 26.0 - - + -
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Residues in contact with LYS 616 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147 ILE* 4.3 13.9 + - - -
157 PHE* 3.6 18.7 - - + -
392G ALA* 3.5 19.5 - - + -
395G HIS* 2.9 45.7 + - - -
396G CYS* 4.1 14.6 - - - -
582G TYR* 3.3 12.9 + - - -
612G TYR* 3.8 31.6 - - + +
613G GLN* 3.3 20.8 + - + +
615G MET* 1.3 76.3 - - - +
617G PHE* 1.3 61.8 + - - +
619G VAL* 3.1 25.3 - - - +
620G ALA 3.2 5.2 + - - -
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Residues in contact with PHE 617 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157 PHE* 5.3 2.7 - - - -
467 ILE* 3.5 30.5 - - + -
477 ALA* 4.6 1.6 - - + -
507 THR* 3.2 30.3 - - + -
613G GLN 2.9 14.3 + - - +
614G LYS* 3.2 33.7 - - + +
616G LYS* 1.3 74.7 - - - +
618G ASN* 1.3 75.3 + - - +
619G VAL 3.0 1.8 - - - -
620G ALA* 2.9 25.1 + - + +
621G MET* 3.1 48.6 + - + +
623G ILE* 5.5 1.3 - - + -
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Residues in contact with ASN 618 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614G LYS* 2.8 23.7 + - - +
615G MET 3.2 5.3 + - - +
617G PHE* 1.3 88.1 - - - +
619G VAL* 1.3 57.6 + - - +
621G MET* 3.2 4.1 + - - +
622G GLY 2.8 25.8 + - - -
623G ILE* 3.0 39.9 + - + +
624G GLY 3.1 23.6 + - - +
625G VAL 3.2 18.8 + - - -
627G ASP* 3.3 26.2 + - - +
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Residues in contact with VAL 619 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392G ALA* 4.6 0.4 - - + -
393G TRP* 4.3 10.3 - - + +
396G CYS* 3.6 31.2 - - + -
552G TYR* 3.1 41.3 - - + +
553G LEU* 4.1 9.0 - - + -
556G CYS* 4.0 17.0 - - + -
615G MET 3.1 17.7 - - - +
616G LYS* 3.1 16.6 - - - +
617G PHE 3.0 0.2 - - - -
618G ASN* 1.3 78.5 - - - +
620G ALA* 1.3 63.0 + - - +
621G MET 3.3 0.5 + - - -
622G GLY 3.5 1.2 + - - -
625G VAL* 3.5 22.4 - - + -
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Residues in contact with ALA 620 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117 GLU* 5.9 0.2 - - - -
157 PHE* 3.1 41.0 - - + -
397 GLU 4.9 0.2 - - - +
427 VAL* 5.5 0.4 - - + -
437 GLY* 3.0 21.6 - - - -
467 ILE* 3.7 9.9 - - + -
552G TYR* 3.8 13.5 - - - +
616G LYS 3.2 1.6 + - - +
617G PHE* 2.9 12.4 + - - +
619G VAL* 1.3 79.8 - - - +
621G MET* 1.3 75.9 + - + +
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Residues in contact with MET 621 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437 GLY* 3.3 30.5 - - - +
447 GLU* 4.7 8.5 - - - +
467 ILE* 3.4 27.8 - - + -
477 ALA* 3.6 20.0 - - - -
552G TYR* 4.8 2.6 - - - +
555G HIS* 5.5 1.9 - - - -
617G PHE* 3.1 41.7 + - + +
618G ASN* 3.4 12.3 - - - +
619G VAL 3.2 0.2 - - - -
620G ALA* 1.3 92.7 - - + +
622G GLY* 1.3 59.3 + - - +
623G ILE* 3.7 20.4 - - + -
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Residues in contact with GLY 622 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552G TYR* 3.9 16.4 - - - -
555G HIS* 2.8 33.0 - - - +
556G CYS 4.0 0.2 - - - -
559G ARG* 2.8 29.8 + - - -
618G ASN 2.8 7.6 + - - -
619G VAL 3.5 1.6 + - - -
621G MET* 1.3 76.8 - - - +
623G ILE* 1.3 57.7 + - - +
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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