Contacts of the strand formed by residues 489 - 495 (chain T) in PDB entry 2P8Z
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 489 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487T PRO 3.3 0.2 - - - -
488T VAL* 1.3 87.8 - - + +
490T GLN* 1.3 62.6 + - - +
491T VAL* 5.8 0.9 - - + -
531T ALA* 3.1 1.6 - - - -
532T GLY 2.6 38.9 + - - +
534T GLY* 3.7 30.3 - - - +
535T GLU* 3.7 22.4 - - + +
538T LEU* 3.6 23.0 - - + +
781T THR* 4.4 15.9 - - + -
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Residues in contact with GLN 490 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487T PRO* 3.1 22.0 + - - +
488T VAL 3.9 7.3 + - - +
489T VAL* 1.3 80.1 - - - +
491T VAL* 1.3 68.6 - - - +
519T LEU* 4.7 1.6 - - - +
521T TYR* 2.7 31.8 + - - -
529T ILE* 3.8 8.7 - - + -
530T VAL 3.3 7.0 - - - +
531T ALA* 3.3 20.2 - - + +
538T LEU* 4.4 0.4 - - - -
559T PRO* 3.7 19.9 - - + +
778T PHE* 5.4 4.3 - - - -
1700T SO1 3.4 36.0 + - - +
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Residues in contact with VAL 491 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489T VAL* 5.8 1.1 - - + -
490T GLN* 1.3 80.6 - - - +
492T ALA* 1.3 60.2 + - - +
493T VAL* 3.9 4.1 + - + +
529T ILE* 3.4 8.7 - - - +
530T VAL 3.0 34.0 + - - +
538T LEU* 4.0 15.3 - - + -
542T LEU* 3.7 35.4 - - + -
556T ILE* 3.8 19.3 - - + -
557T SER 3.7 13.0 - - - +
558T PRO* 5.3 2.0 - - + -
559T PRO* 4.4 4.0 - - - -
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Residues in contact with ALA 492 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491T VAL* 1.3 72.3 - - - +
493T VAL* 1.3 62.6 + - - +
527T GLU* 3.5 38.6 - - + +
528T HIS 3.3 9.0 - - - +
529T ILE* 3.9 6.5 - - + -
555T LYS 3.5 5.0 - - - +
556T ILE* 3.6 3.5 - - - +
557T SER* 2.8 41.8 + - - +
558T PRO 4.5 5.5 - - - -
559T PRO* 4.8 0.8 - - + +
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Residues in contact with VAL 493 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491T VAL* 4.2 4.9 - - + +
492T ALA* 1.3 78.8 - - - +
494T GLU* 1.3 67.4 + - - +
504T LEU* 4.0 14.3 - - + +
508T LEU* 5.5 0.2 - - + -
527T GLU* 5.7 0.3 - - - +
528T HIS* 2.9 36.7 + - + +
530T VAL* 3.6 32.1 - - + -
542T LEU* 3.9 10.3 - - + -
545T LEU* 4.1 6.7 - - + -
554T LEU* 3.7 32.8 - - + -
555T LYS 3.6 2.0 - - - -
556T ILE* 3.8 20.4 - - + -
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Residues in contact with GLU 494 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493T VAL* 1.3 79.3 - - - +
495T VAL* 1.3 76.7 + - + +
501T LEU* 5.3 6.1 - - + -
504T LEU* 3.9 8.1 - - - -
528T HIS* 5.6 1.8 - - + -
554T LEU* 3.4 2.9 - - - -
555T LYS* 2.6 63.5 + - - +
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Residues in contact with VAL 495 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494T GLU* 1.3 87.6 - - + +
496T LYS* 1.3 61.9 + - - +
497T ASN 3.4 27.5 - - - +
498T ALA* 3.9 4.7 + - - +
500T ASP* 3.8 12.6 - - + -
501T LEU* 3.6 39.0 - - + +
504T LEU* 3.6 35.3 - - + +
552T VAL* 4.9 1.8 - - + -
553T PRO 3.7 7.4 - - - +
554T LEU* 4.3 6.7 - - + -
555T LYS* 5.1 1.2 - - - +
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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