Contacts of the strand formed by residues 531 - 539 (chain D) in PDB entry 6IWQ
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 531 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481D TYR 4.3 0.2 + - - -
482D ALA* 2.9 37.1 + - - +
485D PRO* 3.0 26.1 - - - +
488D GLN* 5.7 0.2 + - - -
529D PRO 4.6 1.0 - - - +
530D LYS* 1.3 83.0 - - - +
532D VAL* 1.3 63.6 + - - +
533D ASP* 4.3 9.6 - - - +
534D TRP* 4.8 4.7 - - + -
572D ARG* 3.7 21.1 + - - +
573D ILE 3.5 13.9 - - - +
574D ASN* 4.3 5.0 - - - +
575D GLU* 4.6 3.6 - - - +
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Residues in contact with VAL 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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531D ASN* 1.3 75.5 - - - +
533D ASP* 1.3 65.0 + - + +
573D ILE* 2.8 24.5 + - + -
574D ASN 3.8 18.8 - - - +
575D GLU* 3.9 18.8 - - + -
610D TYR* 5.1 14.8 - - + +
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Residues in contact with ASP 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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531D ASN* 3.7 3.1 - - - +
532D VAL* 1.3 81.4 - - + +
534D TRP* 1.3 80.0 + - - +
572D ARG* 3.4 1.0 - - - +
573D ILE* 2.7 32.7 + - + +
610D TYR* 3.7 15.4 - - + -
612D LYS* 2.5 43.8 - - - +
651D MET* 3.9 21.9 - - - +
653D ASN* 3.5 12.0 + - - -
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Residues in contact with TRP 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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485D PRO* 3.1 49.3 - - + +
486D GLU* 3.7 28.3 - - + -
488D GLN* 4.0 15.6 + - + -
531D ASN* 4.8 7.6 - - + +
533D ASP* 1.3 85.5 + - - +
535D GLY* 1.3 62.8 + - - +
570D LEU* 4.0 12.8 - - + -
571D PHE 3.3 12.1 - - - +
572D ARG* 3.8 4.5 - - + -
651D MET* 3.5 8.3 - - - -
652D ASN 3.7 2.3 + - - -
653D ASN* 2.7 64.0 + - + -
654D ILE 3.4 20.4 - - - -
655D HIS* 3.9 21.1 - + - -
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Residues in contact with GLY 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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534D TRP* 1.3 91.2 - - - +
536D GLU* 1.3 66.4 + - - -
537D ILE 3.8 0.9 + - - -
570D LEU* 3.4 11.3 - - - +
571D PHE* 2.8 33.7 + - - +
651D MET* 3.4 4.0 - - - +
652D ASN 3.0 10.8 - - - -
653D ASN* 4.1 0.7 - - - -
654D ILE 4.5 0.7 - - - -
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Residues in contact with GLU 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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535D GLY* 1.3 74.6 - - - -
537D ILE* 1.3 62.4 + - - +
538D ARG* 2.8 47.3 + - + -
545D CYS* 3.8 14.2 - - + -
562D CYS* 4.2 1.2 - - - +
564D ARG* 3.7 18.9 + - - +
569D GLN* 3.2 20.3 - - + +
650D GLU 3.7 0.2 - - - +
651D MET* 3.1 9.4 - - - +
652D ASN* 2.8 60.2 + - - +
654D ILE* 4.1 18.9 - - + +
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Residues in contact with ILE 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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535D GLY 3.8 0.2 + - - -
536D GLU* 1.3 75.8 - - - +
538D ARG* 1.3 57.8 + - - +
545D CYS* 3.5 3.3 - - - +
546D ILE* 3.1 49.8 + - + -
569D GLN 4.2 3.2 + - - -
571D PHE* 3.7 37.5 - - + -
579D LEU* 3.8 24.5 - - + -
617D PHE* 3.6 32.1 - - + -
626D LEU* 5.0 0.7 - - + -
649D TRP* 3.8 20.3 - - + -
650D GLU 3.6 4.7 - - - +
651D MET* 3.8 16.4 - - + -
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Residues in contact with ARG 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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536D GLU* 2.8 39.6 + - - +
537D ILE* 1.3 73.2 - - - +
539D GLY* 1.3 67.1 + - - +
542D THR 3.3 30.0 + - - +
543D ALA* 3.8 14.6 - - - +
544D TYR 3.7 4.0 - - - -
545D CYS* 4.2 2.0 - - - +
562D CYS* 3.5 29.1 - - - +
564D ARG* 3.2 42.6 - - - +
649D TRP* 3.3 9.6 - - - -
650D GLU* 3.1 51.9 + - + +
652D ASN* 4.1 8.7 - - - +
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Residues in contact with GLY 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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538D ARG* 1.3 76.4 - - - +
540D PHE* 1.3 61.8 + - - -
541D GLU 3.1 1.2 + - - -
542D THR* 2.8 43.4 + - - +
544D TYR 2.9 16.0 + - - -
628D ARG* 3.4 22.9 - - - -
649D TRP* 4.0 4.1 - - - -
650D GLU* 4.8 0.2 - - - -
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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