Contacts of the strand formed by residues 843 - 848 (chain D) in PDB entry 3N1Q
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 843 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835D THR* 4.5 0.9 - - - -
836D GLU 4.0 3.1 - - - +
837D ALA* 4.4 9.0 - - + -
838D VAL* 4.5 2.0 - - - +
842D GLN* 1.3 80.1 - - - +
844D MET* 1.3 71.2 + - - +
889D HIS 3.9 0.2 - - - +
890D MET* 3.8 1.9 - - - -
891D ILE* 2.8 46.5 + - + +
894D LEU* 3.7 15.5 - - + +
900D TYR* 4.1 10.8 - - + -
902D ILE* 3.6 23.8 - - + -
921D CYS* 3.7 45.5 - - + +
923D THR* 3.7 26.0 - - + +
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Residues in contact with MET 844 (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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838C VAL* 3.7 17.3 - - + -
844C MET* 3.7 23.8 - - + +
888C TRP* 4.4 6.1 - - + -
890C MET* 4.2 4.5 - - + -
834D TYR* 4.0 6.5 - - + +
835D THR* 3.1 5.7 - - - -
836D GLU 2.8 44.1 + - - +
838D VAL* 3.7 12.5 - - + +
843D ILE* 1.3 73.7 - - - +
845D LEU* 1.3 64.4 + - - +
846D LYS* 5.7 0.2 - - + -
888D TRP* 3.4 37.9 - - + -
889D HIS 3.3 20.9 - - - +
890D MET* 3.5 30.7 - - + -
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Residues in contact with LEU 845 (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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832D ILE* 4.3 17.5 - - + -
834D TYR 3.5 4.0 - - - +
835D THR* 3.7 19.7 - - + -
844D MET* 1.3 75.4 - - - +
846D LYS* 1.3 59.6 + - - +
847D TRP* 3.6 14.9 - - + -
864D ILE* 3.9 21.3 - - + -
888D TRP* 3.3 4.1 - - - -
889D HIS* 3.0 59.4 + - + +
891D ILE* 3.8 25.8 - - + -
902D ILE* 3.9 21.8 - - + -
904D MET* 4.4 3.4 - - + -
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Residues in contact with LYS 846 (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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834C TYR* 4.2 14.8 - - + +
844C MET* 5.4 1.8 - - + -
832D ILE* 3.6 3.1 - - - +
833D ALA* 2.7 46.7 + - + +
834D TYR* 3.1 44.0 + - + +
844D MET* 4.3 0.6 - - + -
845D LEU* 1.3 73.7 - - - +
847D TRP* 1.3 74.6 + - - +
848D THR* 4.1 12.6 - - - -
887D GLN* 3.0 39.8 + - - +
888D TRP* 4.1 14.0 - - + +
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Residues in contact with TRP 847 (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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830D PRO* 4.3 6.5 - - + -
831D HIS 3.3 14.4 - - - +
832D ILE* 3.9 6.1 - - + -
833D ALA 4.0 0.2 - - - +
845D LEU* 3.6 16.8 - - + -
846D LYS* 1.3 95.4 + - - +
848D THR* 1.3 76.8 + - - +
849D TYR* 4.9 1.3 - - + -
862D PHE* 3.5 38.4 - + - -
864D ILE* 4.5 2.5 - - + -
882D VAL* 4.0 14.6 - - + -
886D LYS* 3.1 28.6 + - + -
887D GLN* 3.1 18.8 + - + +
888D TRP 3.6 13.9 - - - -
889D HIS* 3.5 35.2 - - + -
904D MET* 3.4 40.4 - - + -
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Residues in contact with THR 848 (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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830D PRO* 3.6 6.6 - - - +
831D HIS* 2.8 53.6 + - - +
833D ALA* 4.9 8.1 - - + -
846D LYS* 4.1 16.4 - - + +
847D TRP* 1.3 83.7 - - - +
849D TYR* 1.3 63.0 + - - +
887D GLN* 4.7 8.5 - - - +
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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