Contacts of the helix formed by residues 85 - 93 (chain C) in PDB entry 3EHW
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 ARG 85 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ALA* 4.7 0.7 - - - -
159B GLY* 4.1 4.4 - - - -
161B THR* 3.3 7.7 + - - -
162B GLY 2.8 29.7 + - - -
163B LYS* 4.2 5.5 - - - +
777B DUP 2.8 56.2 + - - +
49C ASP* 4.4 5.3 + - - +
83C ALA 3.8 0.2 + - - -
84C PRO* 1.3 75.6 - - - +
86C SER* 1.3 64.8 + - - +
88C LEU* 3.6 23.3 + - + +
89C ALA* 3.1 21.8 + - - +
94C ILE 4.9 0.2 - - - +
128C ARG* 3.0 51.5 + - - +
129C ILE 4.5 1.9 + - - -
130C ALA* 4.0 27.6 - - - +
131C GLN* 3.9 9.0 - - + +
778C MG 4.2 1.0 - - - -
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Residues in contact with SER 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA* 3.7 13.2 - - - +
158B PHE* 3.1 33.4 + - - -
777B DUP 2.7 64.1 + - - -
84C PRO 4.0 0.6 + - - -
85C ARG* 1.3 69.7 - - - +
87C GLY* 1.3 60.3 + - - +
89C ALA* 3.6 0.6 - - - +
90C ALA* 2.8 34.0 + - - +
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Residues in contact with GLY 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PHE* 3.5 26.9 - - - +
159B GLY* 3.7 3.1 - - - -
163B LYS* 5.7 0.7 - - - -
777B DUP 2.7 18.6 + - - -
86C SER* 1.3 72.9 + - - +
88C LEU* 1.3 63.7 + - - +
91C LYS* 2.9 41.8 + - - +
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Residues in contact with LEU 88 (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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163B LYS* 4.2 26.7 - - + +
777B DUP 4.5 0.8 + - - -
85C ARG* 3.6 22.7 + - + +
87C GLY* 1.3 74.8 - - - +
89C ALA* 1.3 57.1 + - - +
92C HIS* 3.0 29.8 + - + +
93C PHE 3.2 0.2 + - - -
94C ILE* 3.2 32.8 + - + +
121C PHE* 3.9 26.9 - - + -
128C ARG 3.9 8.3 - - - +
129C ILE* 3.7 46.7 - - + +
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Residues in contact with ALA 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 3.3 8.3 - - - +
98A ALA* 3.9 28.7 - - + +
112A VAL* 4.4 9.2 - - + -
114A PHE* 4.4 6.5 - - + -
84C PRO* 5.1 0.4 - - + -
85C ARG 3.1 18.2 + - - +
86C SER 3.6 4.0 - - - +
87C GLY 3.2 0.2 - - - -
88C LEU* 1.3 76.8 - - - +
90C ALA* 1.3 59.9 + - - +
93C PHE* 3.0 24.8 + - - -
94C ILE 3.3 21.4 + - - +
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Residues in contact with ALA 90 (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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63A LYS* 2.9 27.8 + - - +
65A VAL* 3.7 29.6 - - + +
112A VAL* 4.6 5.4 - - + -
158B PHE* 3.8 18.6 - - + -
86C SER 2.8 19.5 + - - +
87C GLY* 4.3 0.9 - - - +
89C ALA* 1.3 74.7 - - - +
91C LYS* 1.3 61.5 + - + +
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Residues in contact with LYS 91 (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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63A LYS* 4.0 7.3 + - - -
158B PHE* 3.3 28.6 + - - -
159B GLY* 4.3 12.9 + - - -
163B LYS* 4.3 26.2 - - - +
87C GLY* 2.9 23.5 + - - +
90C ALA* 1.3 81.8 - - + +
92C HIS* 1.3 81.5 + - + +
93C PHE 3.8 0.2 - - - -
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Residues in contact with HIS 92 (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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63A LYS* 4.3 0.9 - - - -
163B LYS* 3.9 21.7 + - - -
88C LEU* 3.0 18.7 + - + +
91C LYS* 1.3 102.2 + - + +
93C PHE* 1.3 72.7 + - - +
94C ILE* 3.2 19.3 + - + +
115C ASN* 3.8 8.7 + - - -
117C GLY* 4.0 4.0 - - - -
121C PHE* 4.1 26.6 - + + -
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Residues in contact with PHE 93 (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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61A MET* 3.6 25.6 - - - -
62A GLU* 3.7 28.9 - - - -
63A LYS* 3.5 19.6 - - + +
114A PHE* 3.2 48.2 - + + -
115A ASN 5.1 0.2 - - - -
116A PHE* 4.0 13.9 - + - -
89C ALA 3.0 16.6 + - - -
92C HIS* 1.3 80.5 - - - +
94C ILE* 1.3 60.7 + - - +
95C ASP 3.9 0.5 + - - -
114C PHE 3.8 0.7 - - - +
115C ASN 4.0 0.2 - - - -
116C PHE* 3.0 58.9 + + + +
117C GLY* 3.5 13.5 - - - +
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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