Contacts of the strand formed by residues 273 - 279 (chain 3) in PDB entry 6Q8W
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 GLU 273 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2433 ARG* 4.4 15.5 + - - +
2693 THR* 3.6 7.4 - - - -
2703 ARG 3.1 41.9 + - - +
2713 SER* 3.9 11.3 - - - +
2723 GLY* 1.3 78.5 - - - +
2743 LEU* 1.3 62.6 + - - +
2753 LEU* 3.4 17.9 + - + +
3023 ASP* 4.1 20.9 - - + +
6293 ILE* 4.7 2.2 - - - -
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Residues in contact with LEU 274 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2433 ARG* 2.9 14.8 + - - -
2673 ALA* 4.7 3.1 - - + -
2683 ASP 3.9 7.2 - - - +
2693 THR* 3.7 22.2 - - + -
2733 GLU* 1.3 72.4 - - - +
2753 LEU* 1.3 61.5 + - - +
2763 ARG 4.7 1.1 - - - +
2773 ILE* 3.8 23.3 - - + -
2983 HIS* 3.5 47.4 + - + +
3013 ALA* 4.1 6.1 - - + -
3023 ASP* 3.3 27.4 - - + +
6083 TYR* 3.7 26.5 - - + -
6293 ILE* 4.2 14.4 - - + +
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Residues in contact with LEU 275 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2393 THR 4.4 0.3 - - - +
2403 ALA* 3.1 20.0 - - + +
2433 ARG* 3.1 55.4 + - + +
2443 ALA* 3.7 25.1 - - + -
2493 MET* 3.7 23.1 - - + -
2683 ASP 2.9 13.1 + - - +
2693 THR 4.4 0.2 - - - -
2703 ARG* 3.6 42.2 - - + +
2733 GLU* 3.4 14.5 + - + +
2743 LEU* 1.3 75.2 - - - +
2763 ARG* 1.3 60.2 + - + +
2983 HIS* 3.5 12.3 - - - -
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Residues in contact with ARG 276 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233 ASP* 4.7 8.7 + - - -
1243 LYS* 6.1 0.8 - - - +
2273 THR* 6.0 3.6 - - - -
2363 LEU* 6.0 4.2 - - - +
2373 ASP* 4.3 15.0 - - + +
2403 ALA* 3.5 21.9 + - + -
2463 ASN* 3.8 35.5 + - - +
2493 MET* 3.2 35.1 - - + +
2683 ASP* 2.8 42.7 + - + +
2743 LEU* 3.9 0.6 - - - +
2753 LEU* 1.3 84.6 - - + +
2773 ILE* 1.3 70.7 + - - +
2783 ARG* 3.4 44.3 - - + +
2983 HIS* 4.4 4.3 - - - -
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Residues in contact with ILE 277 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2373 ASP* 5.3 0.7 + - - +
2653 ILE* 4.4 18.8 - - + -
2663 THR 3.5 3.4 - - - +
2673 ALA* 3.5 34.5 - - + -
2743 LEU* 3.8 14.6 - - + -
2763 ARG* 1.3 80.8 - - - +
2783 ARG* 1.3 76.4 + - - +
2903 ILE* 5.3 0.9 - - + -
2943 GLY 3.9 17.0 - - - +
2953 ARG* 3.5 37.4 + - + +
2983 HIS* 4.1 19.9 + - + -
6083 TYR* 3.9 25.8 - - + +
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Residues in contact with ARG 278 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2283 ASP* 4.2 17.5 + - - +
2463 ASN* 6.1 1.6 - - - +
2513 GLU* 4.3 16.6 + - - -
2653 ILE* 3.4 9.2 - - - +
2663 THR* 2.9 47.1 + - - +
2683 ASP* 2.7 52.3 + - - +
2763 ARG* 3.4 36.4 - - + +
2773 ILE* 1.3 80.3 - - - +
2793 ALA* 1.3 67.8 + - - +
2903 ILE* 4.5 2.5 - - - -
2953 ARG* 3.7 7.6 - - - +
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Residues in contact with ALA 279 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2283 ASP* 3.4 12.9 + - + +
2663 THR* 4.1 5.7 + - - -
2783 ARG* 1.3 82.8 + - - +
2803 ARG* 1.3 58.5 + - - +
2813 GLU 4.2 0.7 + - - -
2883 ILE* 3.1 30.7 - - - +
2893 TRP 4.6 0.2 - - - +
2903 ILE* 3.5 17.5 - - + -
2953 ARG* 3.5 18.2 - - - +
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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