Contacts of the strand formed by residues 797 - 801 (chain A) in PDB entry 3MP6
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 ILE 797 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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745A LEU* 4.7 6.1 - - + -
746A VAL 3.3 2.0 + - - -
747A ILE* 3.4 20.6 - - + -
748A TRP 3.0 24.8 + - - -
795A PRO* 3.6 6.9 - - - +
796A ASP* 1.3 86.4 - - + +
798A ILE* 1.3 61.5 - - - +
799A PHE* 3.6 29.2 - - + -
1002A ALA* 4.0 12.8 - - + -
1003A GLY 3.1 11.2 - - - +
1004A ILE* 4.6 0.7 - - + -
1014A ALA* 3.8 29.2 - - + -
1017A PHE* 4.0 18.4 - - + -
1018A LEU* 4.0 24.0 - - + -
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Residues in contact with ILE 798 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748A TRP* 3.7 5.8 - - + +
781A LEU* 3.7 21.3 - - + -
785A PHE* 3.3 67.5 - - + -
795A PRO* 4.6 2.2 - - + -
796A ASP 4.4 0.2 - - - -
797A ILE* 1.3 73.3 - - - +
799A PHE* 1.3 75.9 + - - +
800A TRP* 5.0 1.3 - - + -
805A PHE* 3.4 13.5 - - + -
808A TYR* 3.8 16.4 - - + +
814A LEU* 4.2 12.1 - - + -
1002A ALA* 3.3 1.4 - - - -
1003A GLY 2.8 42.6 + - - +
1005A ASN 5.6 0.9 - - - +
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Residues in contact with PHE 799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747A ILE* 3.5 26.5 - - + -
748A TRP 2.8 23.7 + - - +
749A ILE* 3.7 37.1 - - + -
750A ASN* 4.5 1.6 + - - +
758A LEU* 4.0 13.9 - - + -
781A LEU* 3.9 5.0 - - - +
797A ILE* 3.6 13.2 - - + -
798A ILE* 1.3 82.2 - - - +
800A TRP* 1.3 73.9 + - - +
846A ILE* 3.9 15.5 - - + -
1000A LEU* 4.4 13.5 - - + -
1001A SER 3.1 13.2 - - - -
1002A ALA* 3.7 15.3 - - + -
1017A PHE* 5.1 0.2 - + - -
1018A LEU* 4.2 3.8 - - + -
1022A LEU* 3.5 32.5 - - + -
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Residues in contact with TRP 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750A ASN* 3.5 40.4 - - + -
781A LEU* 3.8 20.6 - - + -
782A GLU* 3.3 46.7 - - + -
798A ILE* 4.9 4.9 - - + -
799A PHE* 1.3 84.8 - - - +
801A ALA* 1.3 88.4 + - - +
802A HIS 3.6 0.2 + - - -
803A ASP* 4.0 1.1 - - - -
804A ARG* 3.7 19.2 - - + +
805A PHE* 3.7 18.2 - - + -
808A TYR* 5.3 1.1 - - + -
1000A LEU* 4.0 8.2 - - - +
1001A SER* 2.9 30.5 + - - +
1B GLC 4.5 13.7 - - - -
2B GLC 3.0 37.9 + - - -
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Residues in contact with ALA 801 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800A TRP* 1.3 97.3 - - - +
802A HIS* 1.3 65.5 + - - +
803A ASP* 3.0 18.7 + - - +
804A ARG 3.5 3.3 + - - -
805A PHE* 4.3 3.5 - - - -
849A GLU* 4.7 5.6 - - - +
998A GLY* 4.4 7.0 - - - -
999A VAL 3.4 11.2 - - - +
1000A LEU* 4.2 4.7 - - - +
1068A MET* 4.0 10.3 - - + -
1B GLC 3.5 16.0 + - - +
2B GLC 3.4 13.2 - - - +
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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