Contacts of the helix formed by residues 608 - 622 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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581H TRP* 3.8 4.2 - - - -
604H ASP* 4.4 6.5 - - - -
606H GLU 4.3 0.4 - - - -
607H PHE* 1.3 77.7 - - - +
609H LEU* 1.3 71.0 + - - +
610H SER* 2.9 27.8 + - - -
611H VAL* 3.7 12.5 - - - +
612H TYR* 3.6 18.9 + - - +
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Residues in contact with LEU 609 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581H TRP* 4.6 22.2 - - + +
604H ASP* 4.4 15.7 - - - +
608H SER* 1.3 81.8 - - - +
610H SER* 1.3 62.9 + - - +
611H VAL 3.6 0.2 - - - -
612H TYR* 4.0 1.1 - - + -
613H GLN* 2.7 40.9 + - - +
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Residues in contact with SER 610 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608H SER* 2.9 16.5 + - - -
609H LEU* 1.3 76.7 - - - +
611H VAL* 1.3 72.5 + - - +
612H TYR 3.1 1.1 - - - -
613H GLN* 3.5 3.0 + - - +
614H LYS* 3.0 31.9 + - - +
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Residues in contact with VAL 611 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385H GLU* 5.9 1.6 - - - +
606H GLU 5.5 1.6 - - - +
607H PHE* 3.5 33.9 - - + -
608H SER* 3.7 21.0 + - - +
610H SER* 1.3 85.6 + - - +
612H TYR* 1.3 61.3 + - - +
614H LYS* 3.6 9.6 - - + +
615H MET* 3.2 25.4 + - + +
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Residues in contact with TYR 612 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388H MET* 4.0 18.8 - - + -
391H VAL* 3.3 26.7 + - + +
392H ALA* 4.7 4.5 - - + -
581H TRP* 3.4 53.4 - + + -
582H TYR* 2.8 43.2 + + - -
607H PHE* 5.0 0.8 - - + -
608H SER 3.6 10.2 + - - +
609H LEU* 3.9 0.7 - - + +
610H SER 3.1 0.8 - - - -
611H VAL* 1.3 74.9 - - - +
613H GLN* 1.3 84.5 + - - +
614H LYS 3.0 3.6 - - - -
615H MET* 2.8 45.7 + - + +
616H LYS* 3.4 20.6 + - + +
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Residues in contact with GLN 613 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158 PHE 6.1 1.1 - - - +
558 VAL* 6.5 1.3 - - + -
582H TYR* 5.1 1.2 + - - -
609H LEU* 2.7 43.8 + - - +
610H SER* 4.3 2.5 - - - +
612H TYR* 1.3 100.9 - - - +
614H LYS* 1.3 55.9 + - - +
616H LYS* 3.3 20.4 + - + +
617H PHE* 2.9 27.9 + - - +
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Residues in contact with LYS 614 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610H SER 3.0 20.4 + - - +
611H VAL* 3.6 12.6 - - + +
612H TYR 3.0 0.2 - - - -
613H GLN* 1.3 77.7 - - - +
615H MET* 1.3 57.0 + - + +
617H PHE* 3.2 40.7 - - + +
618H ASN* 2.8 24.0 + - - -
627H ASP* 4.0 27.3 + - - +
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Residues in contact with MET 615 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385H GLU 4.4 2.0 - - - +
388H MET* 3.8 20.9 - - + +
389H ALA* 3.7 14.6 - - - -
392H ALA* 4.1 9.4 - - + -
607H PHE* 4.2 16.6 - - + -
611H VAL* 3.2 13.0 - - + +
612H TYR* 2.8 46.5 + - + +
614H LYS* 1.3 75.8 - - + +
616H LYS* 1.3 60.8 + - - +
617H PHE 3.0 5.2 + - - -
618H ASN* 3.2 12.0 + - - +
619H VAL* 3.1 17.7 + - - +
625H VAL* 3.2 25.9 - - + +
626H LEU* 3.6 25.4 - - + -
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Residues in contact with LYS 616 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148 ILE 4.2 6.5 + - - -
158 PHE* 4.7 13.5 - - + +
168 GLY 5.7 0.2 - - - +
392H ALA* 3.5 19.5 - - + +
395H HIS* 2.9 45.6 + - - -
396H CYS* 4.1 18.4 - - - -
582H TYR* 3.3 14.1 + - - +
612H TYR* 3.8 32.1 - - + +
613H GLN* 3.3 21.2 + - + +
615H MET* 1.3 75.4 - - - +
617H PHE* 1.3 61.3 + - - +
618H ASN 3.4 0.2 - - - -
619H VAL* 3.1 25.7 - - - +
620H ALA* 3.2 8.5 + - - +
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Residues in contact with PHE 617 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468 ILE* 4.7 7.6 - - + -
498 CYS* 5.0 4.9 - - + -
508 THR* 2.8 48.7 - - + -
558 VAL* 5.8 9.9 - - + -
613H GLN 2.9 14.5 + - - +
614H LYS* 3.2 33.2 - - + +
615H MET 3.0 0.2 - - - -
616H LYS* 1.3 74.3 - - - +
618H ASN* 1.3 75.0 + - - +
619H VAL 3.0 1.3 - - - -
620H ALA* 2.9 24.6 + - + +
621H MET* 3.1 36.1 + - + +
623H ILE* 5.5 1.3 - - + -
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Residues in contact with ASN 618 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614H LYS* 2.8 24.8 + - - +
615H MET 3.2 4.6 + - - +
617H PHE* 1.3 87.5 - - - +
619H VAL* 1.3 57.2 + - - +
621H MET* 3.4 4.4 - - - +
622H GLY 2.8 24.6 + - - -
623H ILE* 3.0 40.7 + - + +
624H GLY 3.1 23.6 + - - +
625H VAL* 3.2 19.6 + - - -
627H ASP* 3.3 25.0 + - - +
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Residues in contact with VAL 619 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393H TRP* 4.3 10.5 - - + +
396H CYS* 3.6 32.5 - - + -
552H TYR* 3.1 41.9 - - + +
553H LEU* 4.1 8.1 - - + -
556H CYS* 4.0 16.4 - - + -
615H MET 3.1 17.5 - - - +
616H LYS* 3.1 16.6 - - - +
617H PHE 3.0 0.6 - - - -
618H ASN* 1.3 79.4 - - - +
620H ALA* 1.3 62.1 + - - +
621H MET 3.3 0.3 + - - -
622H GLY 3.5 1.2 + - - -
625H VAL* 3.5 22.7 - - + -
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Residues in contact with ALA 620 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158 PHE* 4.2 23.9 - - + -
438 GLY* 4.8 12.6 - - - +
468 ILE* 3.9 29.4 - - + +
552H TYR* 3.8 10.8 - - - +
616H LYS 3.2 7.0 + - - +
617H PHE* 2.9 12.9 + - - +
619H VAL* 1.3 80.1 - - - +
621H MET* 1.3 78.7 + - + +
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Residues in contact with MET 621 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438 GLY 5.8 0.4 - - - +
468 ILE* 3.5 36.3 - - + +
478 ALA* 4.5 9.4 - - - +
508 THR* 3.3 24.2 - - + -
552H TYR* 4.8 2.8 - - - +
555H HIS* 5.6 1.9 - - - -
617H PHE* 3.1 46.2 + - + +
618H ASN* 3.4 12.6 - - - +
620H ALA* 1.3 83.9 - - + +
622H GLY* 1.3 59.2 + - - +
623H ILE* 3.7 20.2 - - + -
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Residues in contact with GLY 622 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552H TYR* 3.9 16.2 - - - -
555H HIS* 2.9 32.2 - - - +
556H CYS 4.0 0.4 - - - -
559H ARG* 2.8 29.8 + - - -
618H ASN 2.8 8.1 + - - -
619H VAL 3.5 1.6 + - - -
621H MET* 1.3 75.7 - - - +
623H ILE* 1.3 57.3 + - - +
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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