Contacts of the strand formed by residues 2787 - 2794 (chain D) in PDB entry 6DKS
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 GLY2787 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445C ARG* 3.7 6.7 - - - -
2783D ASN* 5.5 0.2 - - - -
2784D THR* 3.0 39.3 + - - -
2785D SER 3.5 0.4 - - - -
2786D GLU* 1.3 81.3 - - - +
2788D VAL* 1.3 65.5 + - - -
2789D VAL* 3.9 1.7 - - - +
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Residues in contact with VAL2788 (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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445C ARG* 2.8 27.9 + - - +
473C GLU* 2.9 37.4 + - + +
474C PRO 5.1 5.2 - - - +
186D ALA* 6.0 6.7 - - + +
2781D ARG* 4.3 26.9 - - + -
2782D VAL 3.4 8.5 - - - +
2783D ASN* 3.3 26.2 - - - +
2787D GLY* 1.3 70.2 - - - -
2789D VAL* 1.3 62.4 + - - +
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Residues in contact with VAL2789 (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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434C ILE* 3.8 26.5 - - + -
445C ARG* 3.6 17.3 - - - +
470C TYR* 3.7 41.1 - - + -
471C THR 3.6 11.2 - - - +
472C PRO* 4.6 4.5 - - + -
2781D ARG* 3.4 1.7 - - - -
2782D VAL* 2.8 46.4 + - + +
2784D THR* 3.9 8.3 - - - +
2786D GLU* 4.3 2.9 - - - +
2787D GLY 3.9 1.1 - - - +
2788D VAL* 1.3 80.7 - - - +
2790D LEU* 1.3 63.1 + - - +
2791D LEU* 4.3 3.8 - - + -
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Residues in contact with LEU2790 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469C THR 3.4 4.9 - - - +
470C TYR* 3.6 0.3 - - - -
471C THR* 2.8 57.7 + - + +
473C GLU* 5.2 6.2 - - + +
180D ASP* 5.2 8.7 - - - +
365D GLN* 4.7 2.7 - - - +
2779D GLY* 4.0 8.5 - - - -
2780D LEU 3.6 31.9 - - - +
2781D ARG* 4.0 31.9 - - + +
2789D VAL* 1.3 71.9 - - - +
2791D LEU* 1.3 62.7 + - - +
2792D SER* 3.8 8.8 + - - +
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Residues in contact with LEU2791 (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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388C LEU* 3.5 17.9 - - + +
395C ALA* 3.8 29.4 - - + -
431C VAL* 3.9 14.4 - - + -
468C PHE* 3.8 13.9 - - + -
469C THR 3.5 3.4 - - - -
470C TYR* 3.6 37.7 - - + -
2779D GLY* 3.1 6.4 - - - -
2780D LEU* 2.8 44.6 + - + +
2782D VAL* 3.8 29.6 - - + -
2789D VAL* 4.3 1.1 - - + -
2790D LEU* 1.3 73.5 - - - +
2792D SER* 1.3 59.0 + - - +
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Residues in contact with SER2792 (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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388C LEU* 4.4 4.9 - - - +
468C PHE* 3.6 7.5 - - - -
469C THR* 2.7 56.3 + - - +
471C THR* 4.3 5.5 + - - -
179D LYS* 5.9 5.2 - - - -
2777D GLY 6.1 0.7 - - - -
2778D ALA 5.9 0.2 - - - -
2779D GLY* 4.6 10.8 - - - -
2790D LEU* 4.5 10.7 + - - +
2791D LEU* 1.3 75.0 - - - +
2793D TYR* 1.3 63.0 + - - +
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Residues in contact with TYR2793 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386C LEU* 3.2 52.5 + - + -
387C GLN* 3.5 18.0 + - - -
388C LEU* 3.7 41.9 + - + -
397C LEU* 4.6 6.1 - - + -
467C THR 3.5 13.5 - - - +
468C PHE* 4.2 8.5 - + + +
179D LYS* 3.6 20.2 + - - -
2777D GLY* 3.4 30.8 + - - -
2778D ALA 4.2 9.9 + - - -
2792D SER* 1.3 76.9 - - - +
2794D SER* 1.3 60.0 + - - +
2795D GLY* 3.1 20.0 + - - +
2796D GLN 5.9 0.2 - - - -
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Residues in contact with SER2794 (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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449C GLN* 5.5 3.4 - - - -
465C SER 4.6 2.9 - - - +
466C LEU* 4.1 4.7 - - - +
467C THR* 3.2 42.8 + - - +
468C PHE* 5.1 0.2 - - - +
469C THR* 5.1 6.7 + - - -
179D LYS* 5.2 4.0 - - - +
2793D TYR* 1.3 67.2 - - - +
2795D GLY* 1.3 64.1 + - - +
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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