Contacts of the strand formed by residues 838 - 845 (chain D) in PDB entry 4X52
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 VAL 838 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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788D ALA* 4.0 15.5 - - + -
789D THR 3.3 6.5 - - - +
791D ARG* 4.5 5.2 + - - -
828D HIS* 4.5 9.0 - - + +
831D CYS* 3.6 20.4 - - + -
833D TYR* 3.5 23.3 - - + +
834D ASP 3.4 17.0 - - - +
835D ALA* 3.2 15.9 + - - +
836D LYS 5.0 0.2 - - - +
837D ASN* 1.3 78.3 - - - +
839D VAL* 1.3 73.2 + - - +
892D GLU* 5.7 0.2 - - - -
893D TYR* 3.2 41.8 + - + +
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Residues in contact with VAL 839 (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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787D TYR 4.1 0.3 - - - +
788D ALA* 3.4 3.8 - - - -
789D THR* 2.9 45.9 + - + +
790D SER 4.1 6.3 - - - +
791D ARG* 3.9 36.8 - - + +
794D VAL* 3.6 28.3 - - + -
838D VAL* 1.3 80.5 - - - +
840D MET* 1.4 59.3 + - - +
841D PHE* 4.3 2.7 - - + -
890D VAL* 4.0 11.2 - - + -
891D ILE 3.6 12.3 - - - +
892D GLU* 4.1 14.4 - - + +
893D TYR* 3.9 4.9 - - - -
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Residues in contact with MET 840 (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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747D PHE* 4.1 10.5 - - + -
751D MET* 4.1 7.2 - - + -
786D PHE* 3.6 40.8 - - + -
787D TYR 3.9 1.1 - - - -
788D ALA* 3.8 30.3 - - + -
824D ALA* 3.3 29.4 - - + +
827D SER* 4.1 2.2 - - - -
828D HIS* 3.9 5.6 - - + -
839D VAL* 1.4 71.5 - - - +
841D PHE* 1.3 62.2 + - - +
890D VAL* 3.6 1.6 - - - -
891D ILE* 2.7 53.1 + - + +
893D TYR* 3.6 31.1 - - + +
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Residues in contact with PHE 841 (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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762D ILE* 3.6 24.7 - - + -
786D PHE* 3.5 6.9 - - - -
787D TYR* 2.8 38.5 + - + +
789D THR* 3.7 31.9 - - + -
794D VAL* 3.8 35.2 - - + -
797D ILE* 3.5 36.6 - - + -
798D CYS* 4.0 4.0 - - - -
802D PHE* 3.9 24.0 - + + -
839D VAL* 4.3 4.5 - - + -
840D MET* 1.3 81.9 - - - +
842D VAL* 1.3 58.8 + - - +
843D ALA 4.0 0.4 - - - -
887D PRO* 4.2 2.0 - - + -
889D TYR 3.3 14.1 - - - -
890D VAL* 3.6 14.6 - - + -
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Residues in contact with VAL 842 (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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743D VAL* 3.8 13.9 - - + -
784D LEU* 3.4 41.1 - - + -
785D LEU 3.5 4.3 - - - +
786D PHE* 3.8 13.2 - - + -
841D PHE* 1.3 73.6 - - - +
843D ALA* 1.3 62.3 + - - +
887D PRO* 4.1 1.2 - - - +
888D GLN* 2.9 27.4 + - - +
889D TYR* 2.8 36.7 + - + +
891D ILE* 3.6 33.9 - - + -
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Residues in contact with ALA 843 (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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783D LYS 3.2 2.4 - - - +
784D LEU* 3.5 3.8 - - - -
785D LEU* 2.8 33.3 + - - +
787D TYR* 5.7 0.4 - - + -
802D PHE* 3.8 10.8 - - + -
820D PHE* 3.8 31.2 - - + -
841D PHE* 4.0 0.8 - - + -
842D VAL* 1.3 76.1 - - - +
844D GLN* 1.4 63.0 + - - +
845D VAL* 3.8 5.3 + - + +
885D VAL* 3.8 11.7 - - + -
886D TYR 3.4 11.0 - - - +
888D GLN* 4.8 0.7 - - - -
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Residues in contact with GLN 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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742D ARG* 4.0 14.8 + - - +
771D PHE* 3.3 27.7 - - + -
782D GLY* 3.5 26.9 - - - +
783D LYS 3.5 2.1 - - - -
784D LEU* 3.5 33.0 + - - +
843D ALA* 1.4 70.5 + - - +
845D VAL* 1.3 59.2 + - - +
885D VAL* 3.3 2.4 - - - -
886D TYR* 2.9 40.6 + - + +
888D GLN* 3.1 41.1 + - + +
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Residues in contact with VAL 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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781D GLU 4.3 0.7 - - - +
782D GLY* 3.6 2.1 - - - -
783D LYS* 2.8 42.6 + - - +
785D LEU* 3.8 23.1 - - + -
820D PHE* 3.9 15.7 - - + -
843D ALA* 3.9 22.7 - - + +
844D GLN* 1.3 79.5 - - - +
846D LEU* 1.3 63.2 + - - +
847D VAL* 3.2 17.0 + - + -
877D PHE* 5.4 0.2 - - + -
879D ILE* 3.5 37.2 - - + -
884D GLN 3.4 5.4 - - - +
885D VAL* 4.1 6.1 - - + -
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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