Contacts of the helix formed by residues 530 - 542 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523D MET* 5.6 2.9 - - - -
529D ALA* 1.3 71.3 + - - +
531D VAL* 1.3 61.5 + - - +
532D GLU* 3.4 5.4 - - - +
533D LYS* 3.8 28.3 - - - +
534D SER* 2.6 33.6 + - - -
576D ILE* 5.4 3.1 - - - +
577D PRO* 5.2 12.2 + - - +
596D VAL* 6.3 0.7 - - - -
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Residues in contact with VAL 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499D THR* 3.6 30.5 - - + -
500D ASP* 6.1 0.7 - - - +
503D MET* 4.0 34.3 - - + -
507D PHE* 4.6 11.9 - - + -
523D MET* 6.2 0.7 - - - -
529D ALA* 3.8 7.2 + - + +
530D SER* 1.3 73.5 - - - +
532D GLU* 1.3 77.6 + - - +
534D SER* 3.8 3.9 - - - -
535D GLN* 3.1 24.3 + - + +
572D TYR* 4.8 6.1 - - + -
901D 15X 5.8 0.2 - - - -
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Residues in contact with GLU 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530D SER* 3.4 2.8 - - - -
531D VAL* 1.3 93.7 + - - +
533D LYS* 1.3 62.2 + - - +
535D GLN* 3.4 5.0 + - - +
536D VAL* 3.3 24.8 + - - +
571D TRP* 5.7 0.4 - - + -
572D TYR* 3.6 35.4 - - + +
575D THR* 3.3 38.5 - - - +
576D ILE* 4.1 8.3 - - + -
577D PRO* 3.8 16.3 - - + +
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Residues in contact with LYS 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530D SER* 3.7 24.7 + - - +
531D VAL 3.4 0.4 - - - -
532D GLU* 1.3 79.1 - - - +
534D SER* 1.3 58.1 + - - +
536D VAL* 3.4 6.2 + - + +
537D GLY* 3.1 22.0 + - - -
576D ILE* 4.1 36.9 - - + +
596D VAL* 4.4 10.3 - - + +
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Residues in contact with SER 534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503D MET* 6.3 0.2 - - - -
523D MET* 2.9 41.5 - - - +
530D SER* 2.6 25.3 + - - -
531D VAL* 3.8 5.4 - - - -
533D LYS* 1.3 76.7 - - - +
535D GLN* 1.3 59.9 + - - +
537D GLY* 3.3 0.5 + - - -
538D PHE* 2.8 30.2 + - - +
596D VAL* 3.4 13.3 - - - +
901D 15X 3.3 15.8 + - - -
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Residues in contact with GLN 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495D TYR* 2.6 29.6 + - - +
499D THR* 3.9 15.4 - - + +
503D MET* 5.2 1.0 - - - -
531D VAL* 3.1 18.3 + - - +
532D GLU 3.6 8.3 - - - +
533D LYS 3.3 0.2 - - - -
534D SER* 1.3 73.0 - - - +
536D VAL* 1.3 60.0 + - - +
538D PHE* 3.4 11.4 + - - +
539D ILE* 2.8 36.7 + - - +
572D TYR* 3.9 30.5 - - + -
901D 15X 3.1 62.3 + - - +
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Residues in contact with VAL 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532D GLU 3.3 16.0 + - - +
533D LYS* 3.5 10.1 - - + +
535D GLN* 1.3 76.2 - - - +
537D GLY* 1.3 57.6 + - - +
539D ILE* 3.4 5.4 + - - +
540D ASP* 2.8 33.8 + - - +
569D ARG* 3.3 45.3 - - - +
572D TYR* 4.2 2.9 - - + -
573D GLN* 3.7 42.8 - - + +
576D ILE* 4.7 2.0 - - + -
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Residues in contact with GLY 537 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533D LYS 3.1 14.1 + - - -
534D SER 3.7 2.7 - - - -
535D GLN 3.3 0.2 - - - -
536D VAL* 1.3 74.1 - - - +
538D PHE* 1.3 59.5 + - - +
540D ASP* 4.5 1.8 - - - -
541D TYR* 2.8 50.4 + - - +
596D VAL* 4.0 15.9 - - - -
600D ILE* 3.9 5.8 - - - +
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Residues in contact with PHE 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485D LEU* 4.3 10.3 - - + -
488D PRO* 3.8 16.4 - - + -
534D SER 2.8 21.0 + - - +
535D GLN* 3.5 22.0 - - - +
537D GLY* 1.3 71.3 - - - +
539D ILE* 1.3 58.4 + - - +
542D ILE* 3.1 25.3 + - + +
543D VAL* 3.0 49.8 + - + -
600D ILE* 4.9 2.7 - - - -
604D PHE* 3.7 24.5 - + - -
901D 15X 3.3 75.4 + + + +
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Residues in contact with ILE 539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488D PRO* 4.0 19.3 - - + -
495D TYR* 3.6 21.8 - - + +
535D GLN* 2.8 23.3 + - + +
536D VAL* 3.7 4.3 - - - +
538D PHE* 1.3 74.7 - - + +
540D ASP* 1.3 66.5 + - - +
543D VAL* 4.1 6.3 - - + -
544D HIS* 2.9 44.2 + - + +
545D PRO* 3.6 0.5 - - - +
565D LEU* 4.1 22.0 - - + -
566D GLU* 6.0 0.2 - - - -
568D ASN 4.7 0.2 - - - +
569D ARG* 3.7 50.5 - - + +
572D TYR* 5.4 1.3 - - + -
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Residues in contact with ASP 540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536D VAL* 2.8 26.9 + - - +
537D GLY* 3.9 3.2 - - - +
539D ILE* 1.3 77.4 - - - +
541D TYR* 1.3 76.1 + - + +
544D HIS* 4.7 3.7 - - - +
545D PRO* 3.4 16.8 - - - +
569D ARG* 2.8 45.8 + - - -
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Residues in contact with TYR 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442D HIS* 5.1 0.3 + - - -
443D MET* 4.6 10.2 - - - +
537D GLY* 2.8 34.4 + - - +
540D ASP* 1.3 88.9 - - + +
542D ILE* 1.3 66.1 + - + +
545D PRO* 3.9 10.7 - - - +
596D VAL* 5.6 2.9 - - + -
600D ILE* 3.6 25.1 - - + +
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Residues in contact with ILE 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442D HIS* 3.8 33.9 + - + +
443D MET* 4.7 2.0 - - + -
485D LEU* 3.8 13.0 - - + -
538D PHE* 3.1 32.1 + - + +
540D ASP 3.7 0.8 - - - -
541D TYR* 1.3 81.3 - - - +
543D VAL* 1.3 66.9 + - - +
544D HIS 3.6 0.9 - - - -
545D PRO* 3.6 4.1 - - - +
546D LEU* 3.3 23.2 + - - +
600D ILE* 3.3 40.4 - - + -
604D PHE* 3.1 43.3 - - + -
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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