Contacts of the strand formed by residues 401 - 408 (chain K) in PDB entry 1HZH
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 ALA 401 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260K PRO 4.9 0.7 - - - -
261K LYS* 4.1 27.1 - - + +
264K LEU* 5.6 0.2 - - + -
400K ILE* 1.3 77.2 - - - +
402K VAL* 1.3 63.7 + - - +
405K GLU* 5.4 1.3 - - + +
457K SER 3.7 0.3 - - - +
458K VAL* 3.4 4.7 - - - +
459K MET* 3.0 62.4 + - + +
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Residues in contact with VAL 402 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392K VAL* 4.4 11.2 - - + -
400K ILE* 4.6 8.7 - - + -
401K ALA* 1.3 77.9 - - - +
405K GLU* 1.3 73.4 + - - +
406K TRP* 5.1 0.4 - - - +
419K TYR* 4.0 10.6 - - - -
421K THR* 4.3 15.5 + - + +
437K LEU* 3.9 30.5 - - + -
439K SER* 3.8 26.5 - - - +
456K CYS* 3.8 18.8 - - - -
457K SER 3.2 9.2 - - - +
458K VAL* 4.5 6.3 - - + -
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Residues in contact with GLU 405 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261K LYS* 2.8 42.8 + - - +
401K ALA* 5.4 1.5 - - + +
402K VAL* 1.3 81.9 - - - +
406K TRP* 1.3 67.7 + - - +
407K GLU* 6.3 0.4 - - + -
415K PRO* 5.5 6.8 - - - +
419K TYR* 3.5 19.4 + - - +
456K CYS* 3.5 5.9 - - - -
457K SER* 2.6 49.2 + - - -
459K MET* 3.8 12.1 - - + +
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Residues in contact with TRP 406 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371K THR* 4.8 2.2 - - + -
388K LEU* 3.7 26.5 - - + -
389K THR 3.9 14.4 - - - -
390K CYS* 3.4 33.4 - - + +
402K VAL* 5.3 0.4 - - + -
405K GLU* 1.3 81.1 - - - +
407K GLU* 1.3 62.7 + - - +
415K PRO* 3.9 3.3 - - - +
416K GLU* 3.1 22.6 + - + +
419K TYR* 3.6 44.7 + + + -
439K SER* 3.0 26.1 + - - -
441K LEU* 3.5 39.9 - - + +
454K PHE* 4.2 10.5 - - + -
455K SER 3.2 29.4 - - - -
456K CYS* 4.3 7.8 - - + -
457K SER* 5.4 0.2 - - - -
472K LEU* 4.2 15.7 - - + -
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Residues in contact with GLU 407 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405K GLU* 6.3 0.2 - - + -
406K TRP* 1.3 76.5 - - - +
408K SER* 1.3 66.1 + - - +
411K GLY* 4.1 20.5 + - - -
414K GLN 3.2 19.3 - - - +
415K PRO* 4.2 2.0 - - + -
416K GLU* 3.9 7.4 - - - +
454K PHE* 3.6 3.1 - - - +
455K SER* 2.9 42.6 + - - -
457K SER* 3.4 19.2 + - - +
467K TYR* 3.9 5.9 + - - -
469K GLN* 3.8 17.3 + - - +
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Residues in contact with SER 408 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407K GLU* 1.3 79.4 - - - +
410K ASN* 1.3 86.9 + - - +
411K GLY 3.0 1.8 - - - +
414K GLN* 2.8 26.2 + - - +
416K GLU* 3.4 20.0 - - - +
447K ARG* 4.6 3.1 + - - -
452K ASN* 5.1 2.4 - - - +
453K VAL 2.7 27.6 + - - -
454K PHE* 4.1 12.4 - - - +
455K SER* 5.1 0.4 - - - +
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Residues in contact with ASN 410 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408K SER* 1.3 87.6 + - - +
411K GLY* 1.3 59.3 + - - +
414K GLN* 3.3 12.6 + - + +
447K ARG* 5.5 4.0 - - - +
452K ASN* 5.6 8.8 + - - +
453K VAL* 4.5 6.5 + - - +
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Residues in contact with GLY 411 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407K GLU* 4.1 18.6 + - - -
408K SER* 3.0 2.0 - - - +
410K ASN* 1.3 77.9 - - - +
414K GLN* 1.3 67.8 + - - +
415K PRO* 4.4 2.4 - - - +
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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