Contacts of the strand formed by residues 581 - 586 (chain D) in PDB entry 3HN3
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 VAL 581 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344D TYR* 3.3 19.4 - - + +
525D PHE* 3.6 33.9 - - + -
536D ILE* 3.2 14.8 - - + +
538D GLN 4.8 0.7 - - - +
573D LEU* 4.0 20.0 - - + +
576D LYS* 3.1 32.3 + - + +
577D ARG* 3.3 17.3 - - + +
579D LYS 5.3 0.2 - - - -
580D TYR* 1.3 82.8 - - + +
582D VAL* 1.3 62.2 + - - +
583D GLY 3.6 19.1 - - - +
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Residues in contact with VAL 582 (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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334D SER 3.5 25.1 - - - +
335D GLN* 4.0 1.1 - - - -
336D PHE* 3.8 35.4 - - + +
343D PHE 3.8 6.0 - - - +
344D TYR* 3.3 15.2 - - - -
345D PHE* 2.9 26.2 + - + -
498D VAL* 4.5 4.5 - - + -
535D PRO* 3.8 22.9 - - + -
536D ILE 2.7 15.4 + - - +
537D ILE* 3.8 17.5 - - + -
580D TYR 3.9 0.4 - - - +
581D VAL* 1.3 74.6 - - - +
583D GLY* 1.3 58.3 + - - +
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Residues in contact with GLY 583 (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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344D TYR* 3.4 9.9 - - - -
345D PHE* 3.2 20.0 - - - -
536D ILE 3.6 3.4 + - - -
537D ILE* 3.4 13.7 - - - +
538D GLN* 2.9 22.3 + - - +
581D VAL* 3.6 9.5 - - - +
582D VAL* 1.3 81.4 - - - +
584D GLU* 1.3 63.1 + - - +
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Residues in contact with GLU 584 (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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344D TYR* 2.6 30.3 + - + +
345D PHE* 2.9 15.5 + - - +
346D HIS* 4.3 5.4 - - - -
347D GLY 3.0 21.5 + - - +
538D GLN* 3.3 8.7 - - + +
541D TYR* 4.3 7.8 + - + -
570D HIS* 4.1 6.9 - - - -
573D LEU* 3.8 23.2 - - + +
583D GLY* 1.3 74.5 - - - +
585D LEU* 1.3 64.4 + - - +
586D ILE 4.3 0.2 - - - -
625D ARG* 2.9 43.6 + - - -
626D TYR* 3.5 18.9 - - + +
629D ILE* 4.5 1.3 - - - -
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Residues in contact with LEU 585 (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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345D PHE* 4.4 15.7 - - + -
347D GLY* 3.5 24.0 - - - +
348D VAL 3.8 9.6 - - - +
349D ASN* 3.6 7.9 - - - +
380D ALA* 4.4 10.3 - - + +
381D PHE* 4.8 1.3 - - - -
382D ARG* 4.1 20.0 - - + +
404D ILE* 4.0 24.9 - - + -
537D ILE* 4.4 9.6 - - + -
538D GLN 2.9 8.9 + - - +
539D SER* 3.3 43.7 - - - +
540D GLU* 3.6 5.7 - - - -
541D TYR* 3.8 6.2 - - - -
584D GLU* 1.3 82.3 - - - +
586D ILE* 1.3 64.2 + - - +
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Residues in contact with ILE 586 (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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347D GLY 3.3 5.6 + - - +
348D VAL* 3.7 21.8 - - + -
349D ASN* 3.0 25.6 + - - -
541D TYR* 3.7 26.5 - - + +
542D GLY* 5.1 0.7 - - - -
562D GLN* 5.5 1.1 - - - +
566D LEU* 3.5 35.9 - - + -
585D LEU* 1.3 71.4 - - - +
587D TRP* 1.3 73.6 + - - +
588D ASN* 3.7 7.5 - - - -
606D LYS 5.4 0.2 - - - +
608D ILE* 3.5 32.3 - - + -
622D LEU* 3.6 26.5 - - + -
626D TYR* 4.1 1.6 + - - +
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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