Contacts of the strand formed by residues 451 - 455 (chain D) in PDB entry 6T8O
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 PRO 451 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425D GLU 5.5 1.6 - - - +
426D VAL* 4.4 13.2 - - + +
429D SER* 3.7 26.9 - - - -
430D PRO* 5.7 0.9 - - + -
431D GLU* 3.8 20.1 - - - +
444D GLY 3.7 6.7 - - - +
445D HIS* 3.4 23.8 - - + +
449D GLY 4.1 0.7 - - - +
450D ARG* 1.3 90.9 - - + +
452D ILE* 1.3 66.7 + - - +
453D ILE* 3.8 18.0 + - + +
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Residues in contact with ILE 452 (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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441D LEU 4.0 0.2 - - - +
443D LEU* 3.4 31.8 + - + +
444D GLY 3.0 15.5 + - - +
446D ASP* 4.0 29.8 - - + +
450D ARG* 4.1 4.7 - - + +
451D PRO* 1.3 82.2 - - - +
453D ILE* 1.3 64.9 + - - +
454D THR* 4.0 21.5 + - + +
680D TYR* 4.8 9.9 - - + -
689D ILE* 4.9 9.6 - - + -
691D VAL* 4.4 20.4 - - + -
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Residues in contact with ILE 453 (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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426D VAL* 4.2 10.1 - - + +
429D SER* 3.7 23.3 - - - +
431D GLU* 4.4 18.4 - - + +
432D TYR* 4.1 26.2 - - + -
435D HIS* 4.4 19.4 + - + -
440D PRO* 4.2 12.3 - - + -
441D LEU 3.3 19.3 - - - +
442D ALA* 3.8 19.7 - - + -
451D PRO* 3.8 21.7 + - + -
452D ILE* 1.3 79.0 - - - +
454D THR* 1.3 62.4 + - - +
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Residues in contact with THR 454 (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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435D HIS* 4.6 2.7 - - - -
441D LEU* 3.3 28.4 + - - +
443D LEU* 4.5 6.1 - - - +
452D ILE* 4.0 15.0 + - + -
453D ILE* 1.3 78.5 - - - +
455D ASP* 1.3 65.6 + - - +
456D LEU 3.5 0.7 + - - -
459D MET* 3.3 13.8 - - - +
680D TYR* 3.0 42.9 + - + +
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Residues in contact with ASP 455 (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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435D HIS* 3.7 18.6 + - + +
437D SER* 2.9 38.5 + - - -
439D VAL 3.1 8.7 - - - +
440D PRO* 4.7 0.7 - - - -
454D THR* 1.3 73.2 - - - +
456D LEU* 1.3 70.4 + - - +
457D ALA* 3.2 15.3 + - - +
458D LYS* 3.2 40.1 + - + +
459D MET* 3.6 15.6 + - - +
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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