Contacts of the strand formed by residues 861 - 866 (chain D) in PDB entry 4AY6
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 SER 861 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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832D ILE* 3.2 12.6 - - - -
834D TYR* 3.8 16.6 - - - -
855D LEU* 3.0 19.4 + - - +
858D VAL* 2.7 27.5 + - - -
859D PRO 3.2 4.5 - - - +
860D ASN* 1.3 79.1 - - - +
862D VAL* 1.3 64.8 + - - +
889D ARG* 2.8 40.0 + - - -
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Residues in contact with VAL 862 (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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827D LEU* 5.0 1.8 - - + -
828D PRO* 3.8 33.7 - - + -
831D ALA* 4.3 2.9 - - + -
832D ILE 3.0 2.8 + - - +
833D VAL* 3.8 32.1 - - + -
834D TYR* 3.0 28.6 + - - +
855D LEU* 3.8 6.3 - - - -
860D ASN 5.6 0.2 - - - -
861D SER* 1.3 79.2 - - - +
863D LEU* 1.3 61.0 + - - +
888D ASN 4.1 14.1 - - - +
889D ARG* 3.3 15.5 - - - +
891D ILE* 4.5 14.1 - - + -
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Residues in contact with LEU 863 (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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834D TYR* 3.1 30.7 - - + +
835D CYS 4.5 5.8 - - - +
836D ASN* 4.8 0.7 - - + +
848D LEU* 4.9 2.0 - - + -
851D TRP* 3.6 39.9 - - + -
855D LEU* 3.9 18.3 - - + +
862D VAL* 1.3 75.4 - - - +
864D TRP* 1.3 64.2 + - - +
865D LEU* 3.9 24.5 - - + -
889D ARG 3.0 7.3 + - - -
890D ILE* 3.6 22.4 - - + +
891D ILE* 2.8 29.7 + - - +
912D LEU* 4.2 14.4 - - + -
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Residues in contact with TRP 864 (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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825D TYR* 3.9 31.0 - + + -
827D LEU* 3.7 39.6 - - + +
833D VAL* 3.9 16.8 - - + -
834D TYR 2.7 16.8 + - - +
835D CYS* 3.4 9.0 - - + +
836D ASN 2.9 30.5 + - - +
837D PHE* 3.6 29.6 - + - -
863D LEU* 1.3 73.5 - - - +
865D LEU* 1.3 73.1 + - - +
891D ILE* 3.4 14.8 - - + +
893D SER* 3.2 26.1 + - - +
904D ARG* 3.4 43.7 - - + -
907D LEU* 4.2 8.1 - - + -
908D ALA* 4.3 5.8 - - + -
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Residues in contact with LEU 865 (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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836D ASN* 3.5 28.9 - - + +
840D LEU* 4.8 5.8 - - + -
843D ILE* 4.7 13.9 - - + -
848D LEU* 5.8 0.7 - - + -
851D TRP* 4.3 12.3 - - + -
863D LEU* 3.9 29.6 - - + -
864D TRP* 1.3 87.3 - - - +
866D LEU* 1.3 71.1 + - - +
876D ILE* 4.4 12.8 - - + -
890D ILE* 3.9 16.6 - - + -
891D ILE 2.9 8.4 + - - +
892D PHE* 3.5 28.2 - - + -
893D SER 2.9 23.8 + - - -
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Residues in contact with LEU 866 (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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836D ASN 4.3 2.2 + - - -
837D PHE* 3.4 51.1 - - + +
838D ASN 4.7 3.6 + - - +
840D LEU* 3.4 23.3 - - - +
865D LEU* 1.3 88.0 - - - +
867D ARG* 1.3 60.1 + - - +
868D PHE* 2.9 25.1 + - + -
892D PHE* 4.0 5.5 - - - -
893D SER* 3.4 20.4 - - - +
894D PRO 4.0 1.6 - - - +
895D VAL* 4.9 4.3 - - + -
904D ARG* 3.3 31.6 - - - +
1200D 12V 3.7 19.1 - - + +
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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