Contacts of the helix formed by residues 594 - 605 (chain C) in PDB entry 3IAD
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 ASN 594 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530C SER* 5.3 5.7 + - - -
533C LYS* 6.1 2.0 - - - +
593C GLY* 1.3 72.0 - - - -
595C GLN* 1.3 73.4 + - - +
596C VAL* 3.4 29.6 - - - +
597C SER* 3.1 26.5 + - - +
598C GLU* 3.2 14.3 + - - +
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Residues in contact with GLN 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520C ILE* 5.4 3.6 + - - +
521C SER 4.9 2.2 + - - -
522C PRO* 3.7 12.7 - - + +
523C MET* 3.5 43.0 + - + +
524C CYS 5.0 0.3 + - - -
525C ASP* 4.6 10.7 + - - +
528C ASN* 3.1 43.5 + - - +
529C ALA* 4.5 0.5 - - - -
593C GLY 4.0 2.1 + - - +
594C ASN* 1.3 78.8 - - - +
596C VAL* 1.3 58.0 + - + +
598C GLU* 3.9 14.6 - - - +
599C PHE* 3.0 28.8 + - - +
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Residues in contact with VAL 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523C MET* 4.6 4.3 - - + -
530C SER* 4.9 8.3 - - - +
533C LYS* 4.7 4.9 - - + +
534C SER* 3.7 31.9 - - - +
537C GLY* 4.2 24.5 - - - -
541C TYR* 5.7 2.5 - - + -
594C ASN* 3.2 21.9 + - - +
595C GLN* 1.3 76.8 - - + +
597C SER* 1.3 58.2 + - - +
599C PHE* 3.2 6.9 + - - +
600C ILE* 3.1 35.8 + - + +
901C 15X 3.9 15.9 + - - +
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Residues in contact with SER 597 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594C ASN* 3.1 26.9 + - - +
596C VAL* 1.3 75.3 - - - +
598C GLU* 1.3 62.9 + - - +
600C ILE* 4.0 7.9 - - - +
601C SER* 3.0 27.0 + - - -
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Residues in contact with GLU 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519C GLU* 5.6 1.4 - - - +
522C PRO* 3.7 22.8 - - + +
593C GLY* 4.7 14.9 - - - +
594C ASN 3.2 18.6 + - - +
595C GLN* 3.8 15.5 - - - +
597C SER* 1.3 76.0 - - - +
599C PHE* 1.3 57.6 + - - +
601C SER* 3.7 4.3 - - - -
602C ASN* 3.0 40.3 + - - +
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Residues in contact with PHE 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C PHE* 3.8 28.9 - + - -
522C PRO* 3.7 30.5 - - + +
523C MET* 4.0 9.4 - - + -
524C CYS* 6.1 0.9 - - - -
595C GLN 3.0 19.3 + - - +
596C VAL* 3.2 4.7 + - - +
598C GLU* 1.3 74.3 - - - +
600C ILE* 1.3 61.6 + - - +
602C ASN* 3.2 2.5 + - - -
603C THR* 2.7 52.5 + - + -
604C PHE* 3.7 11.0 - + - -
901C 15X 3.2 71.8 - + - -
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Residues in contact with ILE 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537C GLY 4.1 12.1 - - - +
541C TYR* 3.6 36.6 - - + +
542C ILE* 3.3 30.3 - - + -
596C VAL* 3.1 24.7 + - + +
597C SER* 4.0 6.7 - - - +
599C PHE* 1.3 78.0 - - - +
601C SER* 1.3 60.0 + - - +
604C PHE* 2.9 40.0 + - + +
605C LEU* 3.9 8.0 + - + +
901C 15X 4.1 13.5 - - - +
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Residues in contact with SER 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597C SER 3.0 20.3 + - - -
598C GLU* 3.7 6.1 - - - -
600C ILE* 1.3 80.0 - - - +
602C ASN* 1.3 66.4 + - - +
605C LEU* 3.4 43.5 - - - +
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Residues in contact with ASN 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C SER* 5.5 1.7 - - - -
522C PRO* 4.4 17.7 - - + +
598C GLU* 3.0 26.4 + - - +
599C PHE* 4.1 2.7 - - - +
601C SER* 1.3 82.6 + - - +
603C THR* 1.3 60.7 + - - +
605C LEU 4.6 6.1 - - - +
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Residues in contact with THR 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439C MET* 3.3 18.4 - - + +
440C SER* 3.2 27.3 + - - -
599C PHE* 2.7 46.2 + - + -
602C ASN* 1.3 76.5 - - - +
604C PHE* 1.3 79.6 + - + +
605C LEU 3.6 1.1 - - - -
901C 15X 4.0 22.2 - - + -
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Residues in contact with PHE 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439C MET* 3.3 44.2 - - + +
440C SER* 4.1 1.9 - - - +
442C HIS* 3.8 30.0 + + + +
443C MET* 3.6 20.3 + - + +
485C LEU* 4.5 1.3 - - + -
538C PHE* 3.9 12.3 - + - -
542C ILE* 3.1 42.2 - - + -
599C PHE* 3.7 24.9 - + - -
600C ILE* 2.9 18.8 + - + +
603C THR* 1.3 88.3 - - + +
605C LEU* 1.3 63.4 + - + +
901C 15X 3.6 27.6 - - + -
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Residues in contact with LEU 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C SER* 3.5 18.3 - - - -
443C MET* 3.6 31.9 - - + -
600C ILE* 4.3 6.5 - - + +
601C SER* 3.4 44.7 + - - +
602C ASN 4.6 4.2 - - - +
603C THR 3.6 2.1 - - - +
604C PHE* 1.3 81.2 + - + +
606C ASP* 1.3 63.8 + - - +
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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