Contacts of the helix formed by residues 608 - 622 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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581A TRP* 3.8 4.1 - - - -
604A ASP* 4.3 7.2 + - - -
607A PHE* 1.3 78.6 - - - +
609A LEU* 1.3 70.9 + - - +
610A SER* 2.9 27.3 + - - -
611A VAL* 3.7 12.7 - - - +
612A TYR* 3.6 18.5 + - - +
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Residues in contact with LEU 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A TRP* 4.6 22.0 - - + +
604A ASP* 4.4 15.3 - - - +
608A SER* 1.3 80.8 - - - +
610A SER* 1.3 63.2 + - - +
612A TYR* 4.0 1.1 - - + -
613A GLN* 2.7 41.0 + - - +
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Residues in contact with SER 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608A SER* 2.9 15.7 + - - -
609A LEU* 1.3 76.5 - - - +
611A VAL* 1.3 73.9 + - - +
612A TYR 3.1 1.3 - - - -
613A GLN* 3.5 3.0 + - - +
614A LYS* 3.0 31.4 + - - +
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Residues in contact with VAL 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A GLU* 5.9 1.8 - - - +
606A GLU 5.5 1.8 - - - +
607A PHE* 3.5 33.4 - - + -
608A SER* 3.7 22.3 + - - +
609A LEU 3.6 0.2 - - - -
610A SER* 1.3 86.4 + - - +
612A TYR* 1.3 61.3 + - - +
614A LYS* 3.6 8.7 - - + +
615A MET* 3.2 25.2 + - + +
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Residues in contact with TYR 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A MET* 4.0 18.4 - - + -
391A VAL* 3.3 26.3 + - + +
392A ALA* 4.7 4.3 - - + -
581A TRP* 3.4 53.4 - + + -
582A TYR* 2.8 42.9 + + - -
607A PHE* 5.1 0.8 - - + -
608A SER 3.6 9.8 + - - +
609A LEU* 3.9 0.7 - - + +
610A SER 3.1 0.6 - - - -
611A VAL* 1.3 73.9 - - - +
613A GLN* 1.3 85.2 + - - +
614A LYS 3.0 3.8 - - - -
615A MET* 2.9 46.3 + - + +
616A LYS* 3.4 20.5 + - + +
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Residues in contact with GLN 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151 PHE* 4.8 17.6 - - + +
582A TYR* 5.1 1.4 + - - -
609A LEU* 2.7 37.6 + - - +
610A SER* 4.3 2.0 - - - +
612A TYR* 1.3 100.1 - - - +
614A LYS* 1.3 56.4 + - - +
616A LYS* 3.3 19.7 + - + +
617A PHE* 2.9 27.9 + - - +
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Residues in contact with LYS 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501 THR* 5.8 5.6 - - - -
610A SER 3.0 19.8 + - - +
611A VAL* 3.6 12.3 - - + +
612A TYR 3.0 0.2 - - - -
613A GLN* 1.3 76.8 - - - +
615A MET* 1.3 58.2 + - + +
617A PHE* 3.2 40.5 - - + +
618A ASN* 2.8 23.6 + - - -
627A ASP* 4.0 27.3 + - - +
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Residues in contact with MET 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A GLU 4.4 1.8 - - - +
388A MET* 3.8 21.1 - - + +
389A ALA* 3.7 14.1 - - - -
392A ALA* 4.1 10.5 - - + -
607A PHE* 4.2 16.2 - - + -
611A VAL* 3.2 13.2 - - + +
612A TYR* 2.9 46.3 + - + +
614A LYS* 1.3 76.3 - - + +
616A LYS* 1.3 61.4 + - - +
617A PHE 3.0 4.8 + - - -
618A ASN* 3.2 12.1 + - - +
619A VAL* 3.1 17.1 + - - +
625A VAL* 3.2 26.8 - - + +
626A LEU* 3.6 26.7 - - + -
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Residues in contact with LYS 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141 ILE* 2.9 29.1 + - - -
151 PHE* 3.0 33.8 - - + +
392A ALA* 3.5 19.5 - - + +
395A HIS* 2.9 36.0 + - - -
396A CYS* 4.1 12.3 - - - -
582A TYR* 3.3 13.3 + - - -
612A TYR* 3.8 33.0 - - + +
613A GLN* 3.3 21.8 + - + +
615A MET* 1.3 75.9 - - - +
617A PHE* 1.3 61.3 + - - +
619A VAL* 3.1 20.9 - - - +
620A ALA 3.2 0.5 + - - -
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Residues in contact with PHE 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151 PHE* 5.0 3.6 - - - -
461 ILE* 3.1 45.3 - - + -
471 ALA* 4.2 4.0 - - + -
501 THR* 3.2 27.6 - - + -
613A GLN 2.9 15.0 + - - +
614A LYS* 3.2 33.0 - - + +
616A LYS* 1.3 74.1 - - - +
618A ASN* 1.3 74.7 + - - +
619A VAL 3.0 1.3 - - - -
620A ALA* 2.9 24.3 + - - +
621A MET* 3.1 42.0 + - + +
623A ILE* 5.5 1.3 - - + -
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Residues in contact with ASN 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A LYS* 2.8 24.2 + - - +
615A MET* 3.2 5.6 + - - +
617A PHE* 1.3 87.2 - - - +
619A VAL* 1.3 57.4 + - - +
621A MET* 3.4 3.8 - - - +
622A GLY 2.8 26.2 + - - -
623A ILE* 3.0 40.5 + - + +
624A GLY 3.1 23.1 + - - +
625A VAL* 3.2 19.4 + - - -
627A ASP* 3.3 25.7 + - - +
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Residues in contact with VAL 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A TRP* 4.3 10.1 - - + +
396A CYS* 3.6 32.1 - - + -
552A TYR* 3.1 41.6 - - + +
553A LEU* 4.1 9.0 - - + -
556A CYS* 4.0 16.4 - - + -
615A MET 3.1 18.6 - - - +
616A LYS* 3.1 15.9 - - - +
617A PHE 3.0 0.2 - - - -
618A ASN* 1.3 79.8 - - - +
620A ALA* 1.3 62.4 + - - +
621A MET 3.3 0.3 + - - -
622A GLY 3.5 1.2 + - - -
625A VAL* 3.5 22.9 - - + -
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Residues in contact with ALA 620 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111 GLU* 5.7 0.7 - - - -
151 PHE* 3.2 32.3 - - + -
391 GLU 4.7 0.7 - - - +
421 VAL* 4.5 1.3 - - + +
431 GLY* 3.0 21.3 - - - -
461 ILE* 3.5 24.9 - - + -
552A TYR* 3.8 14.9 - - - +
616A LYS 3.2 1.6 + - - -
617A PHE* 2.9 11.3 + - - +
619A VAL* 1.3 79.3 - - - +
621A MET* 1.3 67.3 + - + +
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Residues in contact with MET 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431 GLY* 2.9 34.2 - - - +
441 GLU* 4.9 6.8 - - - +
461 ILE* 3.6 11.0 - - + -
471 ALA* 3.6 22.7 - - - +
552A TYR* 4.8 2.3 - - - +
555A HIS* 5.6 2.1 - - - -
617A PHE* 3.1 51.1 + - + +
618A ASN* 3.4 11.7 - - - +
619A VAL 3.2 0.2 - - - -
620A ALA* 1.3 92.6 - - + +
622A GLY* 1.3 58.1 + - - +
623A ILE* 3.7 20.9 - - + -
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Residues in contact with GLY 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A TYR* 3.9 17.0 - - - -
555A HIS* 2.9 32.4 - - - +
556A CYS* 4.6 0.2 - - - -
559A ARG* 2.8 23.2 + - - -
618A ASN 2.8 7.9 + - - -
619A VAL 3.5 1.4 + - - -
621A MET* 1.3 74.4 - - - +
623A ILE* 1.3 65.4 + - - +
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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