Contacts of the helix formed by residues 799 - 821 (chain C) in PDB entry 2W4V
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 LYS 799 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796C LYS 4.5 4.4 + - - +
798C TYR* 1.3 83.5 - - - +
800C LYS* 1.3 49.9 - - - +
801C LEU 2.9 0.2 + - - -
802C GLN* 2.3 40.9 + - + +
803C ASP* 2.2 16.5 + - + +
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Residues in contact with LYS 800 (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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796C LYS 5.4 0.6 + - - -
797C ALA* 4.7 21.5 - - + +
798C TYR 4.0 0.8 - - - +
799C LYS* 1.3 61.7 - - - +
801C LEU* 2.2 53.6 - - - +
802C GLN 2.5 6.5 - - - -
803C ASP* 1.2 125.2 + - - +
804C GLN* 2.1 83.5 + - + +
92Y ALA 4.3 1.6 + - - -
95Y MET* 2.2 81.8 + - + +
96Y PHE* 3.6 9.4 - - - +
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Residues in contact with LEU 801 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797C ALA 4.2 7.7 + - - +
798C TYR* 2.5 34.6 + - + +
800C LYS* 2.2 41.5 - - - +
802C GLN* 1.3 59.9 + - + +
804C GLN* 5.2 2.9 - - + -
805C ARG* 3.6 15.8 + - - +
17Z LEU* 2.2 69.5 - - + +
18Z PHE* 5.1 1.8 - - + -
21Z TRP* 3.5 48.6 - - + -
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Residues in contact with GLN 802 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798C TYR 5.0 2.9 - - - +
799C LYS* 2.3 32.3 + - + +
800C LYS 3.1 1.3 - - - -
801C LEU* 1.3 72.7 - - + +
803C ASP* 1.1 62.7 + - - +
805C ARG* 2.8 44.8 + - - +
806C ILE* 2.7 27.1 + - + +
17Z LEU* 5.8 7.5 - - + +
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Residues in contact with ASP 803 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799C LYS* 2.7 14.1 + - + -
800C LYS* 0.4 168.5 + - - +
802C GLN* 1.1 85.7 - - - +
804C GLN* 1.3 51.3 + - - -
806C ILE* 2.8 26.5 - - - +
807C GLY 2.8 2.1 + - - -
95Y MET* 2.5 31.3 - - - +
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Residues in contact with GLN 804 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800C LYS* 2.1 77.8 + - + +
801C LEU* 5.0 2.9 - - + -
803C ASP* 1.3 69.2 - - - +
805C ARG* 1.3 59.8 + - - +
808C LEU* 2.7 58.1 + - - +
95Y MET* 3.1 4.5 - - - -
96Y PHE* 4.7 6.2 - - + +
112Y LEU* 3.3 22.4 - - - +
21Z TRP* 3.4 23.7 - - + -
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Residues in contact with ARG 805 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800C LYS 3.3 2.0 + - - -
801C LEU 3.6 13.1 + - - +
802C GLN* 2.8 35.3 + - - +
804C GLN* 1.3 85.4 + - - +
806C ILE* 1.3 75.0 + - - +
808C LEU* 4.2 3.1 - - - +
809C SER* 3.5 19.5 + - - -
20Z PHE* 5.6 10.5 - - - -
21Z TRP* 5.0 8.5 - - + -
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Residues in contact with ILE 806 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802C GLN* 2.7 22.2 - - + +
803C ASP* 2.8 14.8 - - - +
805C ARG* 1.3 91.5 - - - +
807C GLY* 1.3 81.8 + - - +
808C LEU 2.7 15.3 + - - -
809C SER* 2.6 28.4 + - - +
810C VAL* 2.9 20.3 + - + +
92Y ALA* 5.3 2.7 - - + -
95Y MET* 4.5 2.5 - - + -
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Residues in contact with GLY 807 (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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803C ASP 2.8 5.9 + - - -
806C ILE* 1.3 86.9 - - - +
808C LEU* 1.3 50.3 + - - +
810C VAL* 2.6 21.9 - - - +
811C ILE* 2.8 16.3 - - - +
92Y ALA* 3.0 21.7 - - - +
95Y MET* 2.6 26.5 - - - -
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Residues in contact with LEU 808 (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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804C GLN* 2.7 51.0 + - - +
805C ARG* 4.2 4.9 - - - +
806C ILE 2.7 2.6 + - - -
807C GLY* 1.3 75.7 - - - +
809C SER* 1.3 58.3 + - - +
810C VAL 3.1 1.8 - - - -
811C ILE* 2.7 43.3 - - + +
812C GLN* 2.7 18.5 + - - +
92Y ALA 5.5 1.6 - - - +
95Y MET* 5.5 0.2 - - + -
112Y LEU* 3.5 38.8 - - + +
113Y LEU* 5.6 0.7 - - + +
116Y MET* 4.8 15.7 - - + +
117Y GLY* 5.8 4.0 - - - -
21Z TRP* 5.0 3.8 - - + -
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Residues in contact with SER 809 (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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805C ARG* 3.5 12.7 + - - -
806C ILE* 2.6 25.4 + - - +
808C LEU* 1.3 76.5 - - - +
810C VAL* 1.3 66.6 + - - +
812C GLN* 4.3 6.3 - - - -
813C ARG* 2.6 64.7 + - - +
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Residues in contact with VAL 810 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806C ILE* 2.9 29.8 + - + +
807C GLY 2.6 27.4 - - - +
809C SER* 1.3 83.3 - - - +
811C ILE* 1.3 66.4 + - + +
813C ARG* 3.6 10.3 - - - +
814C ASN* 2.2 48.0 + - - +
84Y ASP* 5.4 7.2 - - - +
88Y THR 5.2 4.9 - - - +
89Y ILE* 5.3 3.8 - - - -
92Y ALA* 2.7 23.8 - - + -
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Residues in contact with ILE 811 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807C GLY 2.8 22.4 - - - +
808C LEU* 2.7 31.0 - - + +
810C VAL* 1.3 85.4 - - + +
812C GLN* 1.3 58.5 + - - +
814C ASN* 2.4 19.2 + - - +
815C ILE* 2.6 38.0 - - + +
92Y ALA* 4.0 12.1 - - + +
93Y PHE* 4.9 2.7 - - + +
113Y LEU* 2.9 44.6 - - + -
141Y TYR* 4.7 17.7 - - + +
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Residues in contact with GLN 812 (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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808C LEU 2.7 17.5 + - - +
809C SER* 4.1 5.6 - - - +
811C ILE* 1.3 79.7 - - + +
813C ARG* 1.3 66.8 + - - +
815C ILE* 3.1 15.2 - - - +
816C ARG* 3.3 29.3 + - - +
116Y MET 5.5 1.6 - - - +
118Y ASP* 2.7 57.7 + - + +
119Y ASN 4.3 1.4 + - - -
120Y PHE* 2.7 43.6 - - + -
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Residues in contact with ARG 813 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809C SER* 2.6 54.3 + - - +
810C VAL* 3.8 12.2 - - - +
812C GLN* 1.3 87.8 - - - +
814C ASN* 1.3 57.2 + - - +
815C ILE 3.3 1.3 - - - -
816C ARG* 3.7 23.4 + - - +
817C LYS* 3.4 23.2 + - - +
118Y ASP* 6.4 0.2 - - + -
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Residues in contact with ASN 814 (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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810C VAL* 2.2 48.4 + - - +
811C ILE* 2.4 17.3 + - - +
813C ARG* 1.3 72.9 - - - +
815C ILE* 1.3 64.8 + - - +
817C LYS* 4.0 11.8 - - - +
818C TRP* 4.1 13.0 + - - +
83Y THR* 5.3 4.9 - - - +
84Y ASP* 3.8 20.9 - - - +
89Y ILE* 4.9 12.3 - - + +
141Y TYR* 5.1 7.1 + - - -
144Y PHE* 6.3 0.8 - - - -
148Y ILE* 4.3 19.5 - - + +
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Residues in contact with ILE 815 (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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811C ILE* 2.6 27.6 - - + +
812C GLN 3.1 12.6 - - - +
814C ASN* 1.3 80.6 - - - +
816C ARG* 1.3 61.2 + - - +
817C LYS 3.0 4.9 - - - -
818C TRP* 3.3 36.2 + - + +
819C LEU* 2.8 35.4 + - + +
113Y LEU* 4.9 6.5 - - + -
120Y PHE* 3.7 19.5 - - + -
128Y THR* 4.1 24.2 - - + -
144Y PHE* 4.2 16.6 - - + -
148Y ILE* 5.3 1.3 - - + -
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Residues in contact with ARG 816 (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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812C GLN* 3.3 32.0 + - - +
813C ARG* 3.8 30.2 + - - +
815C ILE* 1.3 85.1 - - + +
817C LYS* 1.3 53.9 + - - +
819C LEU* 3.5 9.5 - - + +
820C VAL* 2.9 45.0 + - + +
118Y ASP* 3.2 27.5 + - - -
120Y PHE* 5.1 3.1 - - + -
124Y GLU* 4.0 18.2 - - - +
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Residues in contact with LYS 817 (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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813C ARG 3.4 13.6 + - - +
814C ASN* 4.3 9.4 - - - +
815C ILE 3.0 0.2 - - - -
816C ARG* 1.3 75.9 - - - +
818C TRP* 1.3 57.5 + - - +
819C LEU 2.8 7.4 + - - -
820C VAL* 2.7 29.6 - - + +
821C LEU* 2.8 25.9 + - + +
79Y LYS 3.1 17.6 + - - -
80Y LEU* 4.4 7.6 - - - +
81Y SER 3.0 27.7 + - - -
82Y GLY* 3.7 15.1 + - - +
83Y THR* 3.4 35.0 - - - +
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Residues in contact with TRP 818 (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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814C ASN 4.1 11.1 + - - +
815C ILE* 3.3 26.7 + - + +
817C LYS* 1.3 79.6 - - - +
819C LEU* 1.3 68.0 + - + +
821C LEU* 4.0 12.5 - - + +
822C ARG* 2.6 71.0 + - + +
827C TRP* 5.4 10.0 - + - -
127Y MET 5.9 0.9 - - - -
128Y THR* 5.1 5.2 - - - -
131Y GLU* 4.3 22.9 - - + -
144Y PHE* 3.5 33.7 - + - -
147Y MET* 4.1 9.0 + - + -
148Y ILE* 3.7 46.2 - - + +
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Residues in contact with LEU 819 (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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815C ILE* 2.8 33.4 + - + +
816C ARG* 3.5 8.3 - - - +
818C TRP* 1.3 86.9 - - + +
820C VAL* 1.3 58.1 - - + +
822C ARG* 3.5 15.2 + - + +
823C ASN* 2.5 30.7 + - - +
120Y PHE* 6.0 1.3 - - + -
124Y GLU* 3.8 35.9 - - + +
127Y MET* 3.9 32.8 - - + +
128Y THR* 3.6 26.5 - - + +
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Residues in contact with VAL 820 (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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816C ARG* 2.9 30.0 + - + +
817C LYS* 2.7 32.4 + - + +
819C LEU* 1.3 75.3 - - + +
821C LEU* 1.3 68.2 + - + +
822C ARG 3.2 0.7 - - - -
823C ASN* 3.3 27.5 + - - +
824C TRP* 3.7 7.6 + - - +
124Y GLU* 6.0 0.4 - - - +
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Residues in contact with LEU 821 (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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817C LYS* 2.8 32.2 + - + +
818C TRP* 4.2 12.1 - - + +
819C LEU 3.3 0.2 - - - -
820C VAL* 1.3 81.7 - - + +
822C ARG* 1.3 57.3 + - - +
823C ASN 3.2 2.2 - - - -
824C TRP* 3.3 14.5 - - + +
827C TRP* 3.1 51.1 - - + +
79Y LYS* 4.0 37.5 - - + +
80Y LEU* 3.3 38.8 - - + -
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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
------------------------------------------------------------
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