Contacts of the helix formed by residues 594 - 605 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523B MET* 6.0 0.2 - - - +
533B LYS* 5.3 10.5 - - - +
595B GLN* 1.3 69.8 + - - +
596B VAL* 3.5 20.1 + - - +
597B SER* 3.5 28.8 + - - -
598B GLU* 3.4 33.5 + - - +
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Residues in contact with GLN 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B SER 4.9 0.7 - - - +
522B PRO* 3.8 7.4 - - + +
523B MET* 3.4 45.4 + - + +
524B CYS 4.8 0.9 + - - -
525B ASP* 4.8 7.0 - - - +
528B ASN* 2.7 50.3 + - - +
594B ASN* 1.3 76.0 - - - +
596B VAL* 1.3 59.9 + - - +
598B GLU* 3.7 14.8 - - - +
599B PHE* 2.8 32.4 + - - +
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Residues in contact with VAL 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B MET* 4.2 6.1 - - + -
530B SER* 5.2 2.2 - - - +
533B LYS* 4.4 15.0 - - + +
534B SER* 3.2 36.1 - - - +
537B GLY* 4.2 18.2 - - - -
541B TYR* 5.8 2.5 - - + -
594B ASN* 3.4 18.7 + - - +
595B GLN* 1.3 78.5 - - - +
597B SER* 1.3 57.3 + - - +
599B PHE* 3.4 4.4 + - - +
600B ILE* 3.0 47.5 + - + +
901B 15X 4.4 6.9 + - - +
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Residues in contact with SER 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594B ASN* 3.5 19.5 + - - -
595B GLN 3.3 0.2 - - - -
596B VAL* 1.3 77.0 - - - +
598B GLU* 1.3 61.3 + - - +
600B ILE* 3.5 6.4 + - - +
601B SER* 2.9 40.1 + - - -
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Residues in contact with GLU 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522B PRO* 3.9 20.5 - - + +
594B ASN 3.4 28.3 + - - +
595B GLN* 3.4 15.7 + - - +
596B VAL 3.3 0.4 - - - -
597B SER* 1.3 75.8 - - - +
599B PHE* 1.3 59.8 + - - +
601B SER* 3.8 4.7 - - - -
602B ASN* 2.9 41.1 + - - +
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Residues in contact with PHE 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B PHE* 3.4 32.8 - + - -
522B PRO* 3.5 31.6 - - + +
523B MET* 3.9 9.6 - - + -
524B CYS* 5.8 1.1 - - - -
595B GLN 2.8 22.1 + - - +
596B VAL 3.7 4.0 - - - +
598B GLU* 1.3 72.7 - - - +
600B ILE* 1.3 63.6 + - - +
602B ASN* 4.9 0.4 - - - -
603B THR* 2.7 45.1 + - - -
604B PHE* 3.8 13.0 - + - -
901B 15X 3.3 76.3 - + - +
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Residues in contact with ILE 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B MET* 5.9 3.4 - - + -
537B GLY 3.9 23.1 - - - +
541B TYR* 4.3 18.4 - - + -
542B ILE* 3.4 31.9 - - + -
596B VAL* 3.0 36.9 + - + +
597B SER* 3.9 6.3 - - - +
599B PHE* 1.3 74.6 - - - +
601B SER* 1.3 66.1 + - - +
604B PHE* 3.2 29.1 + - + +
605B LEU* 4.1 9.2 - - + +
901B 15X 3.8 14.4 - - - +
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Residues in contact with SER 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597B SER* 2.9 27.7 + - - -
598B GLU* 3.8 6.1 - - - -
600B ILE* 1.3 79.8 - - - +
602B ASN* 1.3 69.2 + - - +
603B THR 3.4 0.2 + - - -
605B LEU* 3.5 41.9 - - - +
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Residues in contact with ASN 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B SER* 5.4 2.3 - - - -
522B PRO* 3.5 25.5 - - + +
598B GLU* 2.9 27.2 + - - +
599B PHE* 4.2 3.4 - - - +
601B SER* 1.3 81.5 - - - +
603B THR* 1.3 61.7 - - - +
605B LEU 4.5 5.3 - - - +
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Residues in contact with THR 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B MET* 3.2 13.5 - - + +
440B SER* 3.1 27.8 + - - -
599B PHE* 2.7 35.3 + - + -
602B ASN* 1.3 81.9 - - - +
604B PHE* 1.3 72.6 + - + +
605B LEU 3.5 1.6 - - - -
901B 15X 3.0 46.5 + - + +
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Residues in contact with PHE 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B MET* 3.2 49.7 - - + +
440B SER* 3.9 2.4 - - - +
442B HIS* 3.6 29.3 - - + +
443B MET* 3.6 15.7 + - + +
538B PHE* 3.4 27.8 - + - -
542B ILE* 3.1 40.8 - - + -
599B PHE* 3.8 23.3 - + - -
600B ILE* 3.2 21.1 + - + +
603B THR* 1.3 79.1 - - + +
605B LEU* 1.3 63.4 + - + +
901B 15X 3.9 25.1 - + - -
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Residues in contact with LEU 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B SER* 3.5 13.5 - - - -
443B MET* 3.5 42.8 - - + -
600B ILE* 4.1 9.9 - - + +
601B SER* 3.5 39.7 + - - +
602B ASN 4.5 6.1 - - - +
603B THR 3.5 0.2 - - - -
604B PHE* 1.3 81.5 - - + +
606B ASP* 1.3 66.3 + - - +
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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