Contacts of the helix formed by residues 824 - 834 (chain C) in PDB entry 2W4T
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 TRP 824 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820C VAL 4.1 5.6 - - - +
821C LEU* 3.3 27.1 - - + +
822C ARG 3.2 2.8 + - - -
823C ASN* 1.3 78.6 - - - +
825C GLN* 1.4 59.2 + - + +
826C TRP* 3.1 25.4 - - + +
827C TRP* 2.9 15.7 + - + +
828C LYS* 3.0 10.2 + - - +
62Y GLU* 4.1 27.1 - - + +
75Y ILE* 5.1 7.7 - - + +
79Y LYS* 2.5 60.5 - - + +
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Residues in contact with GLN 825 (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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823C ASN 4.1 1.8 + - - -
824C TRP* 1.4 63.4 - - - +
826C TRP* 1.3 57.8 + - - +
828C LYS* 3.1 12.7 + - + +
829C LEU* 2.8 51.4 + - - +
40Y ILE* 4.5 0.2 - - - +
51Y PRO* 3.0 38.9 - - + +
55Y GLU* 5.2 11.7 - - + +
59Y MET* 2.8 47.0 - - + +
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Residues in contact with TRP 826 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824C TRP* 2.9 20.9 + - + +
825C GLN* 1.3 87.0 + - - +
827C TRP* 1.3 53.7 + - - +
829C LEU* 3.7 3.4 - - - +
830C TYR* 2.7 41.0 + - + +
35Y VAL* 5.4 0.4 - - + -
59Y MET* 4.6 33.1 - - + +
60Y LEU* 5.5 0.2 - - + -
62Y GLU* 6.3 1.3 - - + -
67Y LEU* 3.9 24.2 - - + -
72Y PHE* 2.2 63.9 - + - -
75Y ILE* 3.4 32.3 - - + -
76Y PHE* 3.9 20.8 - + - +
79Y LYS* 3.1 18.8 - - - +
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Residues in contact with TRP 827 (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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818C TRP* 5.4 10.8 - + - -
821C LEU* 3.1 52.0 - - + +
822C ARG* 4.2 27.5 - - + +
824C TRP* 2.9 13.6 + - + +
826C TRP* 1.3 75.3 - - - +
828C LYS* 1.3 60.8 + - - +
830C TYR* 3.2 13.3 - + - +
831C SER* 2.6 45.7 + - - -
76Y PHE* 3.8 35.2 - + - -
79Y LYS* 4.6 4.7 - - + +
80Y LEU* 3.9 32.1 - - + -
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Residues in contact with LYS 828 (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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822C ARG 4.7 11.8 + - - +
824C TRP 3.0 10.1 + - - +
825C GLN* 3.2 16.8 - - + +
827C TRP* 1.3 77.9 - - - +
829C LEU* 1.3 67.3 + - + +
831C SER* 2.4 29.2 + - - +
832C LYS* 2.9 8.7 + - + +
49Y ARG 6.0 2.0 - - - -
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Residues in contact with LEU 829 (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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825C GLN* 2.8 48.4 + - - +
826C TRP* 3.7 3.6 - - - +
828C LYS* 1.3 78.2 - - + +
830C TYR* 1.3 65.3 + - - +
832C LYS* 3.1 24.6 - - + +
833C VAL* 3.0 26.0 + - + +
40Y ILE* 4.6 12.3 - - + +
43Y ILE* 4.9 9.4 - - + -
44Y SER* 4.1 32.3 - - - -
49Y ARG 5.6 2.5 - - - +
51Y PRO* 4.8 2.7 - - + -
59Y MET* 4.4 10.8 - - + -
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Residues in contact with TYR 830 (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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826C TRP* 2.7 28.1 + - + +
827C TRP* 3.2 18.4 - + - +
829C LEU* 1.3 72.4 - - - +
831C SER* 1.3 70.9 + - - +
833C VAL* 2.4 36.8 + - + +
834C LYS* 3.0 11.2 + - + -
16Y GLN 4.6 0.5 + - - -
19Y GLU* 3.5 26.9 + - - +
20Y MET* 4.0 25.6 + - - -
23Y ALA* 3.9 24.7 - - + -
27Y ILE* 6.5 0.2 - - + -
72Y PHE* 4.8 13.7 - + - -
76Y PHE* 4.9 19.7 - + + -
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Residues in contact with SER 831 (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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822C ARG* 6.1 2.5 - - - -
827C TRP* 2.6 29.7 + - - -
828C LYS* 2.4 29.5 + - - +
830C TYR* 1.3 81.0 - - - +
832C LYS* 1.3 58.6 + - - +
834C LYS* 2.9 33.0 - - - +
835C PRO* 4.0 1.2 - - - +
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Residues in contact with LYS 832 (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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828C LYS* 2.9 8.5 + - + +
829C LEU* 3.1 28.9 - - + +
830C TYR 2.9 0.6 + - - -
831C SER* 1.3 85.6 + - - +
833C VAL* 1.3 65.5 + - + +
835C PRO* 3.3 11.8 - - - +
44Y SER* 3.7 7.0 - - - +
47Y LEU* 2.2 57.5 - - + +
48Y GLY* 2.2 37.6 - - - +
49Y ARG 5.8 1.3 - - - +
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Residues in contact with VAL 833 (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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829C LEU* 3.4 14.1 - - + +
830C TYR* 2.4 55.5 + - + +
832C LYS* 1.3 76.2 - - + +
834C LYS* 1.3 72.8 + - - +
835C PRO* 2.6 18.9 - - - +
23Y ALA* 4.5 15.5 - - + -
26Y MET* 5.2 15.0 - - + +
27Y ILE* 4.4 21.3 - - + +
43Y ILE* 5.3 12.3 - - + -
47Y LEU* 4.7 8.6 - - + +
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Residues in contact with LYS 834 (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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830C TYR* 3.0 10.8 + - + +
831C SER* 2.9 22.4 - - - +
833C VAL* 1.3 83.7 - - - +
835C PRO* 1.3 80.6 - - + +
19Y GLU* 4.8 14.2 + - - +
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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