Contacts of the helix formed by residues 74 - 79 (chain C) in PDB entry 6EKK
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 THR 74 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359A THR 4.3 2.7 - - - +
360A GLN* 2.7 28.7 + - - +
361A LEU 4.0 6.7 - - - +
362A GLN* 2.8 31.1 + - - +
365A LYS* 3.8 41.5 - - + -
72C THR* 4.2 0.9 - - + +
73C ILE* 1.3 77.8 - - - +
75C SER* 1.3 65.6 + - - +
76C THR* 3.6 5.4 + - - -
77C TYR* 3.2 20.1 + - - +
78C TYR* 3.6 4.4 - - - -
105C GLU* 4.2 13.5 - - - +
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Residues in contact with SER 75 (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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360A GLN* 2.7 37.1 + - - +
74C THR* 1.3 74.4 - - - +
76C THR* 1.3 66.9 + - - +
77C TYR 3.1 0.7 + - - -
78C TYR* 3.1 14.0 + - - +
79C ARG* 3.8 9.4 + - - +
105C GLU* 4.9 3.2 + - - +
109C ASN* 4.0 13.7 - - - -
110C CYS* 3.6 27.8 - - - -
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Residues in contact with THR 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLU* 2.6 36.0 + - + +
225A HIS* 4.6 2.4 + - - -
243A MET* 4.8 0.5 - - - -
244A PRO* 3.5 17.1 - - - +
360A GLN* 3.2 27.6 + - + +
361A LEU* 4.2 7.0 - - + -
74C THR* 3.3 4.2 + - - -
75C SER* 1.3 78.6 + - - +
77C TYR* 1.3 64.1 + - - +
78C TYR 3.2 0.9 + - - -
79C ARG* 3.5 57.6 + - - +
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Residues in contact with TYR 77 (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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225A HIS* 3.3 37.5 - + + +
242A PRO 4.8 0.2 - - - -
243A MET* 3.7 42.8 + - + +
244A PRO* 3.8 5.8 - - - -
12C LEU* 3.7 34.1 - - + +
13C ILE 4.9 0.7 + - - -
14C ILE* 3.9 19.0 - - + +
63C ASP* 4.5 1.9 - - - -
64C THR* 2.9 37.4 + - + +
67C GLN* 3.3 12.3 + - + -
70C PHE* 5.5 2.2 - + - -
73C ILE* 3.7 24.0 - - + -
74C THR 3.2 14.7 + - - +
75C SER 3.1 0.4 - - - -
76C THR* 1.3 83.2 + - - +
78C TYR* 1.3 64.6 + + + +
79C ARG 3.4 1.6 + - - +
81C THR* 4.8 0.3 + - - -
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Residues in contact with TYR 78 (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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12C LEU* 3.6 17.3 - - + -
14C ILE* 3.3 23.6 - - + +
73C ILE* 3.7 31.9 + - + +
74C THR 3.6 21.1 - - - -
75C SER 3.1 5.7 + - - +
76C THR 3.1 1.2 - - - -
77C TYR* 1.3 80.2 - + + +
79C ARG* 1.3 65.4 + - - +
80C GLY 3.2 0.5 + - - -
81C THR* 3.1 22.0 + - - +
84C VAL* 3.6 39.7 - - + -
102C TRP* 4.7 2.9 + - - +
105C GLU* 6.0 0.7 - - + -
106C ILE* 3.6 28.0 - - + +
110C CYS* 3.7 26.7 - - + -
113C VAL* 4.5 15.4 - - + +
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Residues in contact with ARG 79 (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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193A TYR* 2.9 36.7 + - - +
194A GLU 3.0 19.2 + - - -
195A ARG* 3.6 28.0 - - - +
196A ARG* 3.1 25.6 + - - +
242A PRO* 3.2 15.3 - - - +
244A PRO* 5.1 0.2 - - - +
361A LEU* 5.7 0.4 - - - +
75C SER 3.8 4.8 + - - +
76C THR* 3.6 42.6 + - - +
77C TYR 3.4 1.6 - - - +
78C TYR* 1.3 77.7 - - - +
80C GLY* 1.3 61.7 + - - +
81C THR* 3.4 0.5 + - - -
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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