Contacts of the strand formed by residues 838 - 845 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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788C ALA* 3.9 15.5 - - + -
789C THR 3.3 7.2 - - - +
791C ARG* 4.4 4.9 + - - -
828C HIS* 4.5 7.4 - - + +
831C CYS* 3.6 21.5 - - + +
833C TYR* 3.5 23.1 - - + +
834C ASP 3.4 17.0 - - - +
835C ALA* 3.3 17.3 + - - +
836C LYS 3.6 0.2 - - - -
837C ASN* 1.3 78.2 - - - +
839C VAL* 1.3 72.7 + - - +
892C GLU* 5.0 0.9 - - - +
893C TYR* 3.3 41.4 + - + +
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Residues in contact with VAL 839 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788C ALA* 3.4 4.3 - - - -
789C THR* 2.9 38.6 + - + +
790C SER 4.1 6.1 - - - +
791C ARG* 3.9 22.7 - - + +
794C VAL* 3.5 29.6 - - + -
838C VAL* 1.3 79.6 - - - +
840C MET* 1.3 59.5 + - - +
841C PHE* 4.1 9.8 + - + -
890C VAL* 4.0 12.3 - - + -
891C ILE 3.6 10.3 - - - +
892C GLU* 3.6 32.5 - - - +
893C TYR* 3.9 4.3 - - - -
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Residues in contact with MET 840 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747C PHE* 4.1 10.1 - - + -
751C MET* 4.2 4.0 - - + -
786C PHE* 3.6 41.5 - - + -
787C TYR 3.9 1.3 - - - -
788C ALA* 3.8 24.9 - - + -
824C ALA* 3.3 31.9 - - + +
827C SER* 4.2 1.1 - - - -
828C HIS* 3.9 10.5 - - + -
839C VAL* 1.3 72.6 - - - +
841C PHE* 1.3 63.0 + - - +
890C VAL* 3.5 1.8 - - - -
891C ILE* 2.7 53.5 + - + +
893C TYR* 3.6 33.8 - - + +
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Residues in contact with PHE 841 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762C ILE* 3.6 24.9 - - + -
786C PHE* 3.5 6.8 - - - -
787C TYR* 2.7 39.3 + - + +
789C THR* 3.7 31.9 - - + -
794C VAL* 3.8 33.9 - - + -
797C ILE* 3.5 36.1 - - + -
798C CYS* 3.9 3.1 - - - -
802C PHE* 3.9 25.1 - + + -
839C VAL* 4.2 4.7 - - + -
840C MET* 1.3 80.6 - - - +
842C VAL* 1.3 59.6 + - - +
843C ALA 4.0 0.4 - - - -
887C PRO* 4.2 1.8 - - + -
889C TYR 3.3 13.2 - - - -
890C VAL* 3.7 14.8 - - + -
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Residues in contact with VAL 842 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743C VAL* 3.8 13.5 - - + -
784C LEU* 3.4 41.5 - - + -
785C LEU 3.5 4.0 - - - +
786C PHE* 3.8 14.4 - - + -
841C PHE* 1.3 74.0 - - - +
843C ALA* 1.3 63.8 + - - +
887C PRO* 3.9 1.4 - - - +
888C GLN* 2.8 27.6 + - - +
889C TYR* 2.8 36.4 + - + +
891C ILE* 3.6 31.0 - - + -
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Residues in contact with ALA 843 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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783C LYS 3.2 2.4 - - - +
784C LEU* 3.5 4.2 - - - -
785C LEU 2.8 32.9 + - - +
787C TYR* 5.7 0.7 - - + -
802C PHE* 3.8 11.2 - - + -
820C PHE* 3.8 21.1 - - + -
841C PHE* 4.0 0.6 - - + -
842C VAL* 1.3 75.0 - - - +
844C GLN* 1.4 62.8 + - - +
845C VAL* 3.9 4.8 - - + +
885C VAL* 3.8 21.8 - - + -
886C TYR 3.4 11.2 - - - +
888C GLN* 4.8 0.4 - - - -
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Residues in contact with GLN 844 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742C ARG* 3.9 15.1 + - - +
771C PHE* 3.2 28.1 - - + -
782C GLY* 3.5 28.1 - - - +
783C LYS 3.5 1.3 - - - -
784C LEU* 3.5 32.8 + - - +
843C ALA* 1.4 70.7 + - - +
845C VAL* 1.3 61.0 + - - +
885C VAL* 3.4 2.9 - - - +
886C TYR* 2.9 40.8 + - + +
888C GLN* 3.1 40.6 + - + +
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Residues in contact with VAL 845 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781C GLU 4.3 0.5 - - - +
782C GLY* 3.7 1.8 - - - -
783C LYS* 2.8 39.3 + - - +
785C LEU* 3.7 27.6 - - + -
820C PHE* 3.9 15.9 - - + -
843C ALA* 3.9 23.6 - - + +
844C GLN* 1.3 78.6 - - - +
846C LEU* 1.3 62.8 + - - +
847C VAL* 3.2 17.7 + - + +
877C PHE* 5.3 0.2 - - + -
879C ILE* 3.5 36.8 - - + -
884C GLN 3.5 5.2 - - - +
885C VAL* 4.1 5.4 - - + -
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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