Contacts of the strand formed by residues 64 - 69 (chain O) in PDB entry 4C4K
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 LEU 64 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14O THR* 6.0 0.2 - - - +
30O SER* 4.1 11.4 - - - +
31O CYS* 3.4 30.3 - - - +
32O GLN* 4.2 8.1 - - + +
60O GLN* 3.4 4.2 - - - +
61O ASP* 2.9 38.8 + - + +
62O GLY 3.3 0.2 - - - -
63O ASP* 1.3 84.3 + - - +
65O TYR* 1.3 61.2 + - - +
66O ARG* 3.7 9.9 - - - +
1105O EDO 3.3 29.2 - - - +
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Residues in contact with TYR 65 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O LEU 4.0 0.2 - - - +
30O SER* 3.2 6.6 - - - -
31O CYS* 3.0 33.7 + - - +
33O ILE* 3.8 33.9 + - + -
38O THR* 3.8 11.6 - - - +
39O PRO* 3.8 18.4 + - - +
41O VAL* 3.5 39.7 - - + +
43O TRP* 4.1 5.2 - - - +
59O ALA 3.6 3.1 - - - -
60O GLN* 3.5 44.9 + - + -
62O GLY 4.0 2.7 + - - -
63O ASP* 3.4 27.2 - - - -
64O LEU* 1.3 72.9 - - - +
66O ARG* 1.3 61.4 - - - +
1104O EDO 3.9 22.9 - - - +
1105O EDO 4.6 0.4 - - - -
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Residues in contact with ARG 66 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19O PHE* 5.2 2.4 - - - -
28O THR* 3.1 46.0 + - - +
29O LEU 3.3 4.3 - - - +
30O SER* 3.6 23.1 + - - -
43O TRP* 4.2 1.8 - - - -
57O ARG 4.2 1.1 - - - +
58O LEU* 3.3 4.0 - - - +
59O ALA* 2.8 34.5 + - + +
64O LEU* 3.7 14.3 - - - +
65O TYR* 1.3 75.0 - - - +
67O LEU* 1.3 58.7 + - - +
68O THR* 3.6 14.4 - - - +
1104O EDO 2.7 19.8 + - - -
1105O EDO 3.0 47.4 + - - +
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Residues in contact with LEU 67 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28O THR* 3.5 0.9 - - - -
29O LEU* 2.8 48.3 + - + +
43O TRP* 3.8 42.1 - - + +
50O VAL* 3.9 21.3 - - + -
56O PHE* 4.2 7.0 - - + -
57O ARG 3.4 14.6 - - - +
58O LEU* 3.9 14.6 - - + -
66O ARG* 1.3 72.3 - - - +
68O THR* 1.3 68.9 + - - +
69O ILE* 4.1 9.3 + - + -
80O TYR* 3.9 31.6 - - + -
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Residues in contact with THR 68 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O ASP* 5.5 2.0 - - + -
27O ALA 3.4 12.3 - - - +
28O THR* 3.0 21.1 + - - -
55O ARG 3.5 2.9 - - - +
56O PHE* 3.6 2.3 - - - -
57O ARG* 2.8 46.6 + - + +
66O ARG* 3.6 14.6 - - - +
67O LEU* 1.3 71.8 - - - +
69O ILE* 1.3 64.8 + - - +
70O LEU* 3.8 26.5 - - + -
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Residues in contact with ILE 69 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O ASP* 3.4 5.7 - - - +
27O ALA* 2.8 38.6 + - + +
29O LEU* 4.5 10.5 - - + -
55O ARG* 3.3 11.0 - - - +
56O PHE* 3.8 27.1 - - + -
67O LEU* 4.2 11.9 - - + +
68O THR* 1.3 77.4 - - - +
70O LEU* 1.3 63.1 + - - +
72O LEU* 3.8 21.0 - - + +
76O ASP* 3.8 15.9 - - - +
80O TYR* 3.5 40.4 - - + +
97O LEU* 3.9 15.7 - - + -
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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