Contacts of the strand formed by residues 448 - 455 (chain H) in PDB entry 1P8J
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 ARG 448 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276E ARG* 3.8 0.4 - - - -
4049E SO4 3.2 37.8 + - - -
445H ALA* 5.5 2.6 - - - +
446H PRO* 3.3 41.1 + - - +
447H GLN* 1.3 81.3 - - - +
449H LYS* 1.3 62.2 + - - +
478H PRO 3.2 27.3 + - - -
479H ASN* 3.7 13.2 - - - +
480H HIS 3.8 14.6 - - - +
481H ILE* 3.6 16.4 - - + -
571H TYR* 3.4 5.2 - - - -
572H GLY 2.7 38.9 + - - +
573H THR* 4.1 7.0 - - - -
574H ALA* 4.7 13.6 + - - +
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Residues in contact with LYS 449 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E LEU* 4.3 6.4 + - - +
272E GLU* 2.6 45.2 + - - +
273E ALA* 5.0 1.0 - - - +
276E ARG* 3.6 37.2 - - - +
275H PHE* 6.1 1.2 - - - -
448H ARG* 1.3 73.2 - - - +
450H CYS* 1.3 61.9 + - - +
451H ILE* 3.9 25.8 + - + +
479H ASN* 3.0 29.1 + - - +
569H VAL* 4.0 18.4 - - + -
570H LEU 3.4 3.8 - - - -
571H TYR* 3.4 34.5 + - + -
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Residues in contact with CYS 450 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449H LYS* 1.3 73.0 - - - +
451H ILE* 1.3 64.5 + - - +
452H VAL* 4.7 6.7 - - - -
471H VAL* 5.8 0.2 - - - -
473H ALA* 3.5 10.3 - - - -
474H CYS* 2.1 58.1 - - - -
479H ASN 3.8 12.1 - - - +
481H ILE* 4.0 8.9 - - + +
568H LEU 3.6 2.4 - - - +
569H VAL* 3.4 2.4 - - - -
570H LEU* 2.7 53.5 + - + +
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Residues in contact with ILE 451 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E ALA* 4.0 20.2 - - + -
237E ALA* 3.8 31.6 - - + +
238E ARG* 3.6 38.8 + - + +
269E LEU* 4.1 10.1 - - + -
449H LYS* 3.9 33.8 + - + +
450H CYS* 1.3 78.2 - - - +
452H VAL* 1.3 64.5 + - - +
453H GLU 5.1 0.2 - - - +
474H CYS* 4.3 3.3 - - - -
567H THR* 3.8 22.4 - - + -
568H LEU 3.8 2.7 - - - -
569H VAL* 4.6 7.9 - - + +
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Residues in contact with VAL 452 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E GLN* 6.1 0.4 - - - -
450H CYS* 4.4 11.0 - - - +
451H ILE* 1.3 78.7 - - - +
453H GLU* 1.3 66.0 + - - +
454H ILE* 3.4 22.1 + - + -
469H LYS* 5.3 2.5 - - + -
471H VAL* 4.4 22.4 - - + -
567H THR* 3.6 3.4 - - - -
568H LEU* 2.8 67.7 + - + +
570H LEU* 4.7 5.8 - - + -
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Residues in contact with GLU 453 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E VAL* 4.9 1.9 - - - +
178E GLN* 3.8 21.2 + - - +
232E THR* 3.0 29.1 + - - +
234E ALA* 3.5 30.0 - - + +
235E VAL* 3.9 16.2 + - - +
238E ARG* 4.6 7.8 + - - +
451H ILE* 5.3 0.7 - - + -
452H VAL* 1.3 75.4 - - - +
454H ILE* 1.3 65.1 + - - +
455H LEU 3.7 7.3 - - - +
456H VAL* 6.1 0.3 - - - +
469H LYS* 5.0 3.5 - - - +
566H PHE 4.2 3.6 - - - -
567H THR* 4.6 7.2 - - - +
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Residues in contact with ILE 454 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452H VAL* 3.5 30.3 - - + +
453H GLU* 1.3 73.5 - - - +
455H LEU* 1.3 59.4 + - + +
456H VAL* 4.0 4.4 + - - +
467H VAL* 3.8 15.6 - - + +
469H LYS* 3.6 51.5 + - + +
471H VAL* 4.4 6.1 - - + -
547H TRP* 5.9 1.8 - - + -
566H PHE* 2.9 63.0 + - + +
568H LEU* 4.1 14.1 - - + -
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Residues in contact with LEU 455 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453H GLU* 3.7 8.6 - - - +
454H ILE* 1.3 78.8 - - - +
456H VAL* 1.3 65.1 + - - +
457H GLU 3.6 19.3 - - - +
458H PRO* 4.8 0.2 - - + -
459H LYS* 4.3 19.5 - - + +
467H VAL* 4.1 30.1 - - + -
563H LEU* 3.7 34.1 - - + +
564H THR 3.9 5.8 - - - +
565H LYS* 3.8 21.3 - - - +
566H PHE* 3.9 19.9 + - + +
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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