Contacts of the strand formed by residues 443 - 450 (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 443 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327D ARG* 2.9 15.8 + - - -
393D MET* 4.2 9.4 - - - -
403D VAL* 3.6 15.5 - - + +
405D ASP* 3.8 39.5 - - + +
437D ASP* 4.4 6.1 - - + +
440D HIS* 3.1 25.1 + - + +
442D ALA* 1.3 73.6 - - + +
444D VAL* 1.3 58.7 + - - +
445D MET 3.9 8.7 - - - +
446D TRP* 4.1 11.4 - - + -
477D ARG* 2.7 43.6 + - - +
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Residues in contact with VAL 444 (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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288D TRP* 5.3 1.1 - - + -
327D ARG* 4.4 2.5 - - - +
329D VAL* 3.6 26.5 - - + +
336D PHE* 3.9 9.8 - - + -
338D ILE* 4.2 10.5 - - + -
345D PHE* 4.0 28.3 - - + -
402D VAL* 4.0 27.1 - - + -
403D VAL 3.1 12.2 + - - +
441D PRO 4.0 8.7 - - - +
442D ALA 3.5 12.1 - - - +
443D VAL* 1.3 75.4 - - - +
445D MET* 1.3 62.5 + - + +
477D ARG* 4.1 5.6 - - - +
478D PRO* 3.1 25.6 - - - +
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Residues in contact with MET 445 (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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336D PHE* 4.2 9.4 - - + -
345D PHE* 4.7 1.1 - - + -
403D VAL 3.6 1.7 + - - +
404D ILE* 3.4 27.8 - - + -
405D ASP 3.0 25.3 + - - +
443D VAL* 3.7 6.6 - - - +
444D VAL* 1.3 85.4 - - + +
446D TRP* 1.3 75.1 + - - +
477D ARG* 4.6 1.8 - - - -
478D PRO* 3.6 29.4 - - + +
479D VAL 4.7 0.9 - - - -
480D THR* 3.8 24.5 - - + -
498D VAL* 3.9 28.7 - - + -
500D CYS* 4.4 1.8 - - - -
537D ILE* 4.0 27.1 - - + -
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Residues in contact with TRP 446 (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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404D ILE* 4.7 0.2 - - - -
405D ASP* 3.4 42.2 - - + -
430D MET* 4.2 8.1 - - + -
433D VAL* 3.9 20.0 - - + -
434D VAL* 4.0 30.3 - - + -
437D ASP* 4.0 23.8 - - + -
438D LYS* 4.4 1.1 - - - -
443D VAL* 4.1 7.4 - - + -
445D MET* 1.3 75.5 - - - +
447D SER* 1.3 59.7 + - - +
470D THR* 3.7 29.5 - - + +
474D ASP* 3.0 34.7 + - + +
477D ARG* 3.6 26.8 - - + +
478D PRO 3.1 17.2 + - - +
479D VAL* 3.3 8.9 - - + +
480D THR* 2.8 29.3 + - - +
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Residues in contact with SER 447 (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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404D ILE* 3.9 17.5 - - - +
405D ASP 3.0 9.0 + - - +
406D GLU* 2.8 34.8 + - - +
407D CYS* 3.1 26.5 + - - +
430D MET* 4.5 2.5 - - - +
445D MET 4.1 0.4 + - - -
446D TRP* 1.3 74.2 - - - +
448D VAL* 1.3 60.2 + - - +
449D ALA 3.2 14.4 + - - -
480D THR* 3.2 11.4 - - - -
481D PHE* 3.8 5.4 - - - -
482D VAL* 4.0 4.6 - - - +
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Residues in contact with VAL 448 (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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407D CYS* 2.9 14.7 - - - -
409D GLY* 4.0 0.2 - - - -
426D HIS* 2.8 28.6 + - - +
430D MET* 4.2 8.5 - - + -
447D SER* 1.3 74.2 - - - +
449D ALA* 1.3 60.4 + - - +
463D LEU* 4.1 14.4 - - + -
466D VAL* 3.7 22.2 - - + -
467D ILE* 3.9 17.3 - - + -
470D THR* 3.8 17.5 - - - +
479D VAL* 3.7 26.9 - - + -
480D THR 2.9 15.6 + - - +
481D PHE* 3.7 11.9 - - + -
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Residues in contact with ALA 449 (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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406D GLU* 3.8 4.2 - - - +
407D CYS 5.0 1.3 - - - -
409D GLY* 3.1 18.8 - - - +
412D LEU* 5.0 1.6 - - + -
426D HIS* 4.6 3.8 - - + -
447D SER* 3.2 10.4 + - - -
448D VAL* 1.3 85.2 - - - +
450D ASN* 1.3 61.1 + - - +
451D GLU 4.3 0.4 - - - -
452D PRO* 4.0 24.2 - - + -
463D LEU* 4.1 15.5 - - + -
481D PHE* 3.8 3.1 - - + +
482D VAL 2.9 25.1 + - - -
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Residues in contact with ASN 450 (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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382D ARG* 2.8 20.6 + - - +
385D HIS* 3.3 37.9 + - - +
406D GLU* 3.6 7.2 + - - +
409D GLY 3.0 9.0 + - - +
410D VAL* 3.8 30.4 - - + +
411D GLY 4.1 3.6 + - - -
449D ALA* 1.3 73.4 - - - +
451D GLU* 1.3 90.7 + - - +
452D PRO* 3.3 2.4 - - - +
482D VAL* 3.5 5.2 - - - +
502D ASN* 3.5 16.6 + - - -
540D GLU* 4.3 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