Contacts of the strand formed by residues 68 - 75 (chain C) in PDB entry 3E8C
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 HIS 68 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ILE* 3.7 31.3 - - + +
59C LEU* 4.2 10.5 - - + +
60C VAL 3.3 7.9 + - - +
61C LYS* 4.2 17.8 - - + +
66C GLY 3.9 11.5 + - - -
67C ASN* 1.3 74.1 - - - +
69C TYR* 1.3 71.6 + - - +
122C TYR* 4.3 9.5 + - + +
321C PRO* 3.9 30.8 - - + +
322C GLY* 3.8 32.1 + - - -
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Residues in contact with TYR 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C PHE* 4.2 4.5 - + - -
59C LEU* 3.7 5.7 - - - +
60C VAL* 2.9 36.4 + - + +
62C HIS* 3.5 30.4 - + + -
65C THR* 4.9 0.2 + - - -
67C ASN* 3.5 36.4 + - + -
68C HIS* 1.3 79.0 - - - +
70C ALA* 1.3 60.6 + - - +
107C GLU* 3.6 31.3 + - + -
108C PHE* 4.1 20.9 - + - -
119C VAL* 3.5 24.5 - - + -
120C MET 3.4 16.2 - - - +
121C GLU* 4.7 4.3 - - - -
122C TYR* 3.9 10.1 - - - -
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU* 4.3 11.9 - - + -
57C VAL* 4.3 4.5 - - + -
58C MET 3.4 6.3 - - - +
69C TYR* 1.3 74.4 - - - +
71C MET* 1.3 61.6 + - - +
119C VAL* 3.4 3.8 - - - +
120C MET* 2.8 56.9 + - + +
121C GLU 4.0 1.6 - - - +
122C TYR* 3.8 4.6 - - - +
351C G96 3.8 26.5 - - + +
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Residues in contact with MET 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 4.3 13.2 - - + -
43C PHE* 3.8 34.5 - - + -
45C ARG* 5.3 2.7 - - - -
56C ARG 3.8 0.3 - - - +
57C VAL* 3.4 3.5 - - - -
58C MET* 2.8 44.7 + - + +
60C VAL* 4.1 20.2 - - + -
70C ALA* 1.3 74.8 - - - +
72C LYS* 1.3 68.8 - - - +
73C ILE* 3.7 17.2 + - + +
110C PHE* 4.0 11.0 - - + -
117C TYR* 3.9 18.6 - - + -
118C MET 3.4 8.3 - - - +
119C VAL* 3.7 25.4 - - + -
120C MET* 4.1 0.9 - - - -
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Residues in contact with LYS 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C PHE* 5.2 3.6 - - - -
56C ARG 3.6 3.1 - - - -
57C VAL* 4.2 7.9 - - + +
71C MET* 1.3 72.2 - - - +
73C ILE* 1.3 61.2 + - - +
74C LEU* 3.7 28.6 - - + +
91C GLU* 2.6 32.8 + - - +
116C LEU 3.7 0.7 - - - +
117C TYR* 3.4 6.9 - - - -
118C MET* 2.9 47.0 + - + +
120C MET* 3.4 16.3 - - + +
184C ASP* 3.8 4.9 + - - -
186C GLY* 4.8 1.8 - - - -
351C G96 3.5 63.4 + - + +
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Residues in contact with ILE 73 (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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40C LEU* 6.0 0.2 - - + -
45C ARG* 5.3 3.4 - - - -
55C GLY* 3.2 7.1 - - - -
56C ARG* 2.8 39.8 + - + +
58C MET* 4.2 22.4 - - + -
71C MET* 4.0 20.2 - - + +
72C LYS* 1.3 75.6 - - - +
74C LEU* 1.3 64.6 + - - +
75C ASP 5.2 0.2 - - - +
115C ASN* 4.0 20.9 - - + +
116C LEU 3.6 3.1 - - - -
117C TYR* 3.9 31.0 - - + -
335C ILE* 3.7 37.2 - - + -
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Residues in contact with LEU 74 (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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54C PHE* 3.6 20.4 - - + -
72C LYS* 3.7 25.4 - - + +
73C ILE* 1.3 75.8 - - - +
75C ASP* 1.3 62.7 + - - +
76C LYS 3.3 0.5 + - - -
79C VAL* 4.1 15.7 - - + -
88C THR* 4.8 4.5 - - - +
91C GLU* 5.6 0.7 - - - +
115C ASN* 3.1 8.3 - - - -
116C LEU* 2.8 69.1 + - + +
117C TYR 4.8 0.4 - - - +
118C MET* 3.6 29.6 - - + -
351C G96 3.6 30.7 - - + -
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Residues in contact with ASP 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C PHE 2.9 16.8 + - - +
55C GLY* 4.5 2.4 - - - -
73C ILE* 4.1 1.8 + - - +
74C LEU* 1.3 68.2 - - - +
76C LYS* 1.3 58.5 + - - +
77C GLN* 3.0 26.7 + - - +
78C LYS* 3.1 41.1 + - + +
79C VAL* 2.9 29.1 + - - +
114C SER* 3.9 5.6 - - - +
115C ASN* 3.5 15.6 + - - +
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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
------------------------------------------------------------
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