Contacts of the helix formed by residues 88 - 97 (chain C) in PDB entry 6DWN
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 GLY 88 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72C ASP* 3.4 18.3 + - - -
87C SER* 1.3 85.9 - - - +
89C LEU* 1.3 65.3 + - - -
90C ASP 3.6 1.8 - - - -
91C THR 4.1 2.0 - - - -
92C ILE* 3.3 18.0 + - - +
413C GLN* 3.1 19.2 + - - -
414C ILE* 4.0 5.3 - - - +
417C ASP* 5.4 1.6 - - - -
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Residues in contact with LEU 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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88C GLY* 1.3 69.4 - - - -
90C ASP* 1.3 72.7 + - - +
92C ILE* 3.3 2.5 + - + +
93C ARG* 3.0 54.3 + - - +
414C ILE* 4.1 18.5 - - + +
420C LEU* 4.5 17.0 - - + +
446C LYS* 4.1 41.1 - - + +
448C ILE* 3.8 14.4 - - + -
452C MET* 3.5 22.2 - - + -
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Residues in contact with ASP 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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89C LEU* 1.3 81.2 - - - +
91C THR* 1.3 64.3 + - - +
93C ARG* 3.4 23.9 + - - +
94C GLN* 3.2 20.8 + - - +
98C ARG* 4.1 6.3 + - - +
397C LYS* 5.1 9.4 - - - +
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Residues in contact with THR 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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72C ASP* 2.7 37.9 + - + +
73C VAL* 3.8 22.0 - - + -
86C LEU* 5.1 5.1 - - + +
87C SER 3.5 15.3 - - - +
88C GLY 3.8 1.2 + - - -
89C LEU 3.3 0.8 - - - -
90C ASP* 1.3 77.4 - - - +
92C ILE* 1.3 62.5 + - + +
94C GLN* 3.4 16.7 - - - +
95C ALA* 3.5 8.3 + - - +
396C LEU* 4.5 6.8 - - + +
397C LYS* 3.3 36.2 + - + +
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Residues in contact with ILE 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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86C LEU* 3.8 33.4 - - + +
87C SER* 3.7 11.0 - - - +
88C GLY 3.3 19.9 + - - +
89C LEU 3.9 2.7 - - - +
91C THR* 1.3 74.1 - - - +
93C ARG* 1.3 67.3 + - - +
94C GLN 3.1 0.2 - - - -
95C ALA* 3.0 16.4 + - - +
96C LEU* 3.0 39.5 + - + +
409C VAL* 3.6 23.3 - - + -
410C ASN 4.6 2.9 - - - +
414C ILE* 3.6 24.2 - - + -
448C ILE* 6.1 1.8 - - + -
452C MET* 4.1 13.9 - - + -
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Residues in contact with ARG 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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89C LEU* 3.0 52.8 + - - +
90C ASP* 3.5 28.7 + - - +
92C ILE* 1.3 76.8 - - - +
94C GLN* 1.3 61.8 + - - +
97C VAL* 3.2 38.7 + - + +
98C ARG* 3.5 21.2 + - - +
445C GLU 4.9 6.7 + - - -
448C ILE* 5.3 0.2 - - - +
452C MET* 3.9 23.0 - - - +
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Residues in contact with GLN 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 ASP 3.2 8.5 + - - +
91C THR* 3.4 13.9 - - - +
92C ILE 3.1 0.4 - - - -
93C ARG* 1.3 79.2 - - - +
95C ALA* 1.3 55.8 + - - +
98C ARG* 2.5 52.8 + - - +
99C GLN* 2.7 65.0 + - - +
396C LEU* 3.2 26.9 - - + -
397C LYS* 5.5 4.5 - - - -
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Residues in contact with ALA 95 (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 LEU* 4.1 17.0 - - + -
91C THR 3.5 3.1 + - - +
92C ILE 3.0 7.4 + - - +
94C GLN* 1.3 81.0 - - - +
96C LEU* 1.3 62.2 + - + +
99C GLN* 2.9 30.2 - - - +
100C GLY* 3.7 0.9 - - - -
103C PHE* 3.3 37.4 - - + +
396C LEU* 3.7 18.4 - - + -
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Residues in contact with LEU 96 (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 LEU* 5.5 3.4 - - + -
92C ILE* 3.0 35.5 + - + +
95C ALA* 1.3 81.6 - - + +
97C VAL* 1.3 59.7 + - - +
100C GLY* 2.9 19.9 - - - -
103C PHE* 4.3 22.0 - - + +
385C THR* 5.5 0.9 - - + -
388C HIS* 4.3 26.7 - - + +
409C VAL* 4.5 17.0 - - + -
451C GLY* 4.9 2.7 - - - -
452C MET* 3.8 42.6 - - + +
453C GLY* 2.9 17.7 - - - -
454C LYS* 3.8 0.9 + - - +
455C ARG* 6.4 0.4 - - + -
601C HEM 4.9 2.0 - - - +
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Residues in contact with VAL 97 (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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93C ARG* 3.2 30.7 + - + +
96C LEU* 1.3 78.3 - - - +
98C ARG* 1.3 74.5 + - + +
99C GLN 3.2 1.1 - - - -
100C GLY* 3.1 10.7 + - - -
452C MET* 3.9 25.6 - - + -
453C GLY* 4.0 9.9 - - - +
454C LYS* 5.9 1.9 - - - -
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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