Contacts of the helix formed by residues 85 - 94 (chain C) in PDB entry 3G65
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 SER 85 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C SER* 4.4 1.6 + - - +
23C ILE* 3.7 10.3 + - - +
24C ALA* 3.6 20.4 - - - +
27C ALA 2.9 28.3 + - - -
28C LYS* 2.9 7.8 + - - -
30C CYS* 3.3 32.0 + - - +
83C LEU* 3.5 6.5 + - - -
84C THR* 1.3 70.8 - - - +
86C GLU* 1.3 62.5 + - - +
88C LEU* 3.2 14.6 + - - +
89C SER* 3.2 14.1 + - - -
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Residues in contact with GLU 86 (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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24C ALA* 4.6 6.0 + - + +
28C LYS* 4.2 6.7 + - + +
84C THR* 3.1 5.9 + - - +
85C SER* 1.3 78.0 - - - +
87C ASN* 1.3 78.4 + - - +
89C SER* 2.6 26.0 + - - +
90C ARG* 2.8 49.6 + - - +
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Residues in contact with ASN 87 (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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191A LYS 5.1 2.8 + - - -
192A ALA* 5.3 0.6 - - - +
193A MET* 3.3 37.3 + - - +
84C THR* 3.0 29.2 + - - +
86C GLU* 1.3 95.0 - - - +
88C LEU* 1.3 60.7 + - - +
90C ARG* 4.2 4.9 + - - -
91C ALA* 3.2 19.4 + - - +
133C ILE* 3.9 16.0 - - + +
134C PRO* 3.7 28.7 + - - +
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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
----------------------------------------------------------
16C PHE* 5.2 7.9 - - + -
20C SER* 3.4 16.6 - - - +
23C ILE* 5.7 2.5 - - + -
32C LEU* 5.0 8.1 - - + -
41C PHE* 4.2 28.9 - - + -
83C LEU* 4.6 20.2 - - + -
84C THR 3.7 1.8 + - - -
85C SER* 3.2 10.3 + - - +
87C ASN* 1.3 76.2 - - - +
89C SER* 1.3 66.3 + - - +
91C ALA* 3.0 5.2 + - + +
92C LEU* 2.9 47.9 + - + +
103C ILE* 5.4 8.7 - - + -
113C LEU* 5.7 2.0 - - + -
115C VAL* 4.7 7.6 - - + -
133C ILE* 3.7 24.6 - - + +
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Residues in contact with SER 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C SER* 3.1 30.8 + - - -
21C ASN* 3.9 20.2 - - - +
24C ALA* 4.0 9.4 - - - +
85C SER 3.2 6.1 + - - -
86C GLU* 2.6 31.4 + - - +
88C LEU* 1.3 74.9 - - - +
90C ARG* 1.3 62.9 + - - -
92C LEU* 3.0 5.3 + - - +
93C LYS* 2.9 22.6 + - - +
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Residues in contact with ARG 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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158A PRO 4.9 10.3 + - - +
160A SER* 3.6 42.5 + - - +
161A PRO* 5.3 2.9 - - - -
193A MET* 3.2 43.5 + - + +
195A THR* 4.9 5.7 + - - -
86C GLU* 2.8 62.2 + - - +
87C ASN* 4.2 4.0 + - - +
89C SER* 1.3 81.2 + - - +
91C ALA* 1.3 62.6 + - - +
93C LYS* 3.3 25.7 + - + +
94C THR* 4.2 5.5 + - - +
131C HIS* 4.6 6.5 + - + -
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Residues in contact with ALA 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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193A MET* 4.3 1.3 - - - +
87C ASN 3.2 14.5 + - - +
88C LEU* 3.0 13.1 + - + +
90C ARG* 1.3 79.0 - - - +
92C LEU* 1.3 58.1 + - - +
93C LYS 3.7 0.2 + - - -
94C THR* 3.7 13.2 + - - -
95C ALA 4.7 0.2 + - - -
115C VAL* 4.4 15.7 - - + +
117C VAL* 4.4 5.5 - - - +
131C HIS* 3.8 43.5 - - + -
133C ILE* 4.0 12.1 - - + -
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Residues in contact with LEU 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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13C LEU* 5.6 0.4 - - + -
16C PHE* 3.6 34.3 - - + +
17C THR* 3.2 31.0 + - + +
20C SER* 3.5 28.5 - - - -
88C LEU* 2.9 30.4 + - + +
89C SER* 3.0 5.1 + - - +
91C ALA* 1.3 75.6 - - - +
93C LYS* 1.3 63.4 + - - +
94C THR 3.3 2.9 - - - -
95C ALA* 3.2 17.1 + - + +
96C GLN* 4.2 0.7 + - - +
101C LEU* 3.8 31.4 - - + -
115C VAL* 4.3 15.3 - - + -
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Residues in contact with LYS 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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161A PRO* 6.4 0.4 - - - +
17C THR* 4.8 4.9 - - - -
21C ASN* 6.1 0.4 - - - +
89C SER 2.9 10.6 + - - +
90C ARG* 3.3 22.1 + - + +
92C LEU* 1.3 78.9 - - - +
94C THR* 1.3 62.3 + - + +
95C ALA 3.2 0.2 - - - -
96C GLN* 3.1 42.1 - - - +
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Residues in contact with THR 94 (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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157A LEU* 4.5 8.3 - - + +
158A PRO* 3.6 38.4 - - + +
90C ARG 4.2 6.2 + - - +
91C ALA 3.7 12.1 + - - -
93C LYS* 1.3 75.9 - - + +
95C ALA* 1.3 56.9 + - - +
96C GLN 3.1 9.7 + - - -
97C ASN 4.4 2.8 + - - -
98C ALA* 4.2 0.2 - - - +
117C VAL* 4.6 7.4 - - - +
119C LEU* 3.2 34.0 - - - +
129C VAL* 4.6 4.7 - - - +
131C HIS* 3.8 12.0 + - - +
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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