Contacts of the helix formed by residues 86 - 94 (chain C) in PDB entry 3GXM
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 86 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C ALA* 3.1 7.6 + - + +
85C MET* 1.3 76.9 - - - +
87C ASP* 1.3 61.6 + - - +
88C ALA* 3.8 1.4 + - - +
89C ALA* 3.1 18.8 + - - +
90C ALA* 2.9 27.9 + - - +
122C PRO* 4.0 15.9 - - + -
126C CYS* 4.4 3.4 - - - -
128C PHE* 4.0 10.8 - - - -
157C LYS* 4.5 1.1 - - - -
381C TRP* 3.4 38.6 - - + -
382C ASN* 2.5 28.8 + - - +
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Residues in contact with ASP 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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86C THR* 1.3 73.9 - - - +
88C ALA* 1.3 52.3 + - - +
90C ALA* 3.4 6.7 + - - +
91C LEU* 2.7 46.1 + - + +
122C PRO* 5.1 1.9 - - - +
124C ALA 5.3 2.5 - - - +
125C SER* 4.6 0.3 - - - -
126C CYS* 5.8 0.4 - - - -
128C PHE 3.6 9.7 + - - +
129C SER* 2.8 28.5 + - - +
130C ILE 5.0 0.7 - - - +
133C TYR* 2.8 32.9 + - - -
152C GLU* 3.6 19.5 - - + +
156C LEU* 4.9 2.1 - - + +
157C LYS* 3.2 23.7 + - - +
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Residues in contact with ALA 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C THR* 3.8 2.0 - - - +
87C ASP* 1.3 77.2 - - - +
89C ALA* 1.3 64.4 + - - +
91C LEU* 3.2 10.0 + - - +
92C ASN* 3.1 23.2 + - - +
128C PHE* 3.2 22.4 + - + +
384C ALA 4.3 0.2 - - - -
385C LEU* 4.0 15.0 - - + -
391C PRO* 3.4 41.5 - - + +
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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
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84C ALA 3.9 6.7 - - - +
85C MET* 4.6 4.3 - - - -
86C THR* 3.1 22.4 + - - +
88C ALA* 1.3 75.6 - - - +
90C ALA* 1.3 62.6 + - - +
92C ASN* 3.3 2.3 + - - +
93C ILE* 3.0 31.4 + - + +
382C ASN 4.5 0.2 - - - -
383C LEU* 3.7 17.5 - - + +
384C ALA* 3.4 35.6 + - - +
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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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85C MET* 4.3 3.9 - - - -
86C THR 2.9 16.0 + - - +
87C ASP 3.6 4.9 - - - +
89C ALA* 1.3 76.8 - - - +
91C LEU* 1.3 63.4 + - - +
92C ASN 2.9 1.7 + - - -
93C ILE 3.7 0.2 + - - -
94C LEU* 3.1 28.1 + - - +
156C LEU* 3.8 26.0 - - + -
157C LYS* 4.1 11.0 - - + -
160C LEU* 3.5 25.7 - - + +
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Residues in contact with LEU 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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131B ARG* 5.3 15.7 - - - +
151B GLU* 5.0 6.3 - - + +
87C ASP* 2.7 35.9 + - + +
88C ALA* 3.2 10.2 + - - +
90C ALA* 1.3 71.7 - - - +
92C ASN* 1.3 54.2 + - - +
94C LEU* 3.7 5.2 + - + +
95C ALA* 3.4 22.7 + - - +
130C ILE* 3.7 41.1 - - + +
152C GLU* 5.8 1.3 - - + -
156C LEU* 3.8 28.3 - - + -
391C PRO* 4.2 13.2 - - + -
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Residues in contact with ASN 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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88C ALA 3.1 22.3 + - - +
89C ALA* 3.5 5.8 - - - +
90C ALA 2.9 1.2 + - - -
91C LEU* 1.3 69.9 - - - +
93C ILE* 1.3 68.7 + - - +
95C ALA* 3.4 14.2 + - - +
96C LEU* 4.0 1.6 + - - +
384C ALA* 3.9 10.9 + - + -
385C LEU* 3.4 10.1 - - - +
386C ASN* 3.2 32.4 + - - +
390C GLY 2.8 27.9 + - - -
391C PRO* 3.6 6.2 - - - +
404C VAL* 3.4 29.5 - - + +
406C ILE* 4.6 7.6 - - - +
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Residues in contact with ILE 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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85C MET* 4.3 23.1 - - + -
89C ALA* 3.0 27.8 + - + +
90C ALA 4.0 3.4 - - - +
92C ASN* 1.3 77.4 - - - +
94C LEU* 1.3 59.1 + - - +
96C LEU* 3.3 29.4 - - - +
101C GLN* 3.4 27.9 - - + +
104C LEU* 3.8 30.7 - - + -
105C LEU* 4.7 10.1 - - + -
160C LEU* 3.7 27.1 - - + -
383C LEU* 4.6 13.9 - - + -
384C ALA* 4.3 5.6 - - + -
404C VAL* 4.7 0.6 - - - +
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Residues in contact with LEU 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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90C ALA 3.1 21.7 + - - +
91C LEU* 3.9 4.9 - - + +
92C ASN 3.3 0.4 - - - -
93C ILE* 1.3 73.3 - - - +
95C ALA* 1.3 56.9 + - - +
96C LEU 3.2 11.7 + - - +
101C GLN* 3.7 29.5 + - - +
155C LYS 4.3 4.3 - - - +
156C LEU* 3.7 45.3 - - + +
159C PRO* 6.3 2.0 - - + -
160C LEU* 3.9 17.0 - - + -
163C ARG* 4.0 13.2 - - - +
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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