Contacts of the helix formed by residues 530 - 542 (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 SER 530 (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* 4.0 14.3 - - - +
529B ALA* 1.3 70.5 - - - +
531B VAL* 1.3 66.1 + - - +
532B GLU* 3.2 4.3 + - - -
533B LYS* 3.3 32.9 + - - +
534B SER* 3.1 23.2 + - - -
576B ILE* 5.6 0.5 - - - +
577B PRO* 5.2 9.5 - - - +
596B VAL* 5.8 1.8 - - - -
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Residues in contact with VAL 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B THR* 4.0 24.9 - - + -
500B ASP* 5.8 2.7 - - - +
503B MET* 4.1 35.6 - - + +
507B PHE* 4.5 12.3 - - + -
523B MET* 5.3 2.5 - - - -
529B ALA* 3.7 7.0 + - + +
530B SER* 1.3 72.5 - - - +
532B GLU* 1.3 82.6 + - - +
534B SER* 3.4 6.0 + - - -
535B GLN* 3.3 22.2 + - + +
572B TYR* 5.1 3.8 - - + -
901B 15X 6.0 0.2 - - - -
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Residues in contact with GLU 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B SER* 3.3 2.5 + - - +
531B VAL* 1.3 93.1 + - - +
533B LYS* 1.3 63.4 + - - +
534B SER 3.3 0.7 + - - -
535B GLN* 3.3 12.3 + - - +
536B VAL* 3.3 16.1 + - - +
572B TYR* 4.0 25.4 - - + +
575B THR* 3.4 40.2 - - + +
576B ILE* 4.0 21.3 - - + -
577B PRO* 4.1 16.2 - - + +
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Residues in contact with LYS 533 (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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530B SER* 3.3 29.7 + - - +
532B GLU* 1.3 78.8 - - - +
534B SER* 1.3 57.2 + - - +
536B VAL* 3.5 4.1 + - + +
537B GLY* 3.0 22.5 + - - -
576B ILE* 3.9 34.8 - - + +
594B ASN* 5.3 10.7 - - - +
596B VAL* 4.4 15.3 - - + +
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Residues in contact with SER 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B MET* 2.9 29.3 - - - +
530B SER 3.1 14.1 + - - -
531B VAL* 3.6 6.7 - - - -
532B GLU 3.2 0.4 - - - -
533B LYS* 1.3 75.0 - - - +
535B GLN* 1.3 55.5 + - - +
537B GLY* 3.2 1.3 + - - +
538B PHE* 2.7 36.9 + - - +
596B VAL* 3.2 21.4 - - - +
901B 15X 3.4 30.4 + - - -
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Residues in contact with GLN 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B TYR* 2.4 40.3 + - - +
499B THR* 3.7 26.5 - - + +
503B MET* 5.3 0.6 - - - -
531B VAL 3.3 13.3 + - - +
532B GLU 3.3 6.9 + - - +
534B SER* 1.3 72.8 - - - +
536B VAL* 1.3 61.1 + - - +
538B PHE* 3.6 10.1 - - - +
539B ILE* 2.9 37.8 + - - +
572B TYR* 4.1 21.8 - - + -
901B 15X 2.9 54.9 + - - +
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Residues in contact with VAL 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B GLU 3.3 13.0 + - - +
533B LYS* 3.7 9.0 - - + +
534B SER 3.3 0.2 - - - -
535B GLN* 1.3 76.6 - - - +
537B GLY* 1.3 57.3 + - - +
539B ILE* 3.8 6.3 - - - +
540B ASP* 2.9 45.3 + - - +
569B ARG* 3.8 29.4 - - - +
572B TYR* 4.0 4.3 - - + -
573B GLN* 3.6 42.8 - - - +
576B ILE* 4.1 7.9 - - + -
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Residues in contact with GLY 537 (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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533B LYS 3.0 14.6 + - - -
534B SER 3.2 3.8 + - - -
536B VAL* 1.3 76.2 - - - +
538B PHE* 1.3 63.7 + - - +
540B ASP* 4.5 1.3 - - - -
541B TYR* 3.0 43.9 + - - +
596B VAL* 4.2 13.0 - - - -
600B ILE* 3.9 7.2 - - - +
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Residues in contact with PHE 538 (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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485B LEU* 3.7 12.8 - - + -
488B PRO* 4.1 12.1 - - + -
534B SER 2.7 17.5 + - - +
535B GLN* 3.6 17.5 - - - +
537B GLY* 1.3 70.9 - - - +
539B ILE* 1.3 58.5 + - - +
542B ILE* 3.1 25.3 + - + +
543B VAL* 2.9 50.4 + - + -
600B ILE* 4.5 0.2 - - - +
604B PHE* 3.4 27.4 - + - -
901B 15X 3.2 82.2 + + + +
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Residues in contact with ILE 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B PRO* 3.9 25.6 - - + -
495B TYR* 3.6 21.5 - - + +
535B GLN* 2.9 24.8 + - + +
536B VAL* 3.8 3.4 - - - +
538B PHE* 1.3 77.5 - - + +
540B ASP* 1.3 62.5 + - - +
543B VAL* 4.0 5.8 - - - -
544B HIS* 2.8 43.4 + - + +
545B PRO* 3.5 0.3 - - - +
565B LEU* 3.9 21.1 - - + +
566B GLU* 6.0 0.2 - - - -
568B ASN* 4.5 0.9 - - + +
569B ARG* 3.6 49.8 - - + +
572B TYR* 5.4 1.3 - - + -
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Residues in contact with ASP 540 (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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536B VAL* 2.9 30.1 + - - +
537B GLY* 3.3 0.5 + - - -
539B ILE* 1.3 77.5 - - - +
541B TYR* 1.3 78.6 + - + +
544B HIS* 4.7 4.0 + - - +
545B PRO* 3.4 17.8 - - - +
569B ARG* 2.7 47.5 + - - +
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Residues in contact with TYR 541 (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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442B HIS* 5.1 0.9 + - - -
443B MET* 4.8 9.9 - - - +
537B GLY* 3.0 33.1 + - - +
540B ASP* 1.3 92.5 - - + +
542B ILE* 1.3 65.3 + - + +
545B PRO* 3.6 13.1 - - - +
596B VAL* 6.0 2.2 - - + -
600B ILE* 4.3 24.5 - - + -
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Residues in contact with ILE 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B HIS* 3.7 30.3 - - + +
443B MET* 5.4 3.4 - - + -
485B LEU* 3.9 12.8 - - + -
538B PHE* 3.1 30.4 + - + +
540B ASP 3.6 0.8 - - - -
541B TYR* 1.3 82.8 - - - +
543B VAL* 1.3 70.0 + - - +
544B HIS 3.5 0.9 - - - -
545B PRO* 3.5 3.9 - - - +
546B LEU* 3.1 24.3 + - - +
600B ILE* 3.4 35.0 - - + -
604B PHE* 3.1 47.8 - - + -
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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
------------------------------------------------------------
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