Contacts of the helix formed by residues 91 - 98 (chain C) in PDB entry 6R93
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 ASP 91 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62C GLU* 3.9 9.4 - - - +
66C LEU* 4.4 11.1 - - + +
87C ALA 3.4 14.9 + - - +
88C ILE 3.0 5.9 + - - +
89C ARG 4.6 0.7 - - - -
90C ASN* 1.3 78.4 - - - +
92C GLU* 1.3 57.5 + - - +
93C GLU* 3.6 16.5 + - - +
94C LEU* 3.1 42.2 + - + +
95C ASN* 2.8 34.1 + - - +
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Residues in contact with GLU 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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135A ARG* 4.2 22.4 + - - +
136A ALA 5.5 2.3 - - - +
89C ARG 5.7 0.2 - - - -
90C ASN 4.0 3.2 + - - -
91C ASP* 1.3 72.1 + - - +
93C GLU* 1.3 72.0 + - + +
95C ASN* 3.4 14.8 + - - +
96C LYS* 3.0 45.7 + - + +
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Residues in contact with GLU 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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91C ASP* 3.3 15.2 + - - +
92C GLU* 1.3 87.2 + - + +
94C LEU* 1.3 61.5 + - - +
96C LYS* 3.3 6.1 + - + +
97C LEU* 3.0 27.7 + - - +
104D PRO* 4.1 31.9 - - + +
106D GLU* 2.6 37.1 - - - +
107D LEU* 4.1 22.6 - - + +
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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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59C LEU* 5.3 7.0 - - + -
62C GLU* 3.9 18.4 - - - +
63C ILE* 3.4 37.0 - - + -
66C LEU* 3.9 18.2 - - + -
87C ALA 4.7 3.4 - - - +
88C ILE* 4.0 16.6 - - + +
91C ASP* 3.1 28.6 + - + +
93C GLU* 1.3 77.0 - - - +
95C ASN* 1.3 58.2 + - - +
97C LEU* 3.7 19.0 - - + +
98C LEU* 2.8 39.6 + - + +
66D PHE* 5.4 3.4 - - + -
107D LEU* 4.7 12.3 - - + -
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Residues in contact with ASN 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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135A ARG* 5.3 14.3 - - - +
88C ILE* 3.6 14.9 + - - +
89C ARG* 3.6 35.3 + - - +
91C ASP 2.8 18.8 + - - +
92C GLU* 3.6 19.9 + - - +
94C LEU* 1.3 77.2 - - - +
96C LYS* 1.3 59.7 + - - +
98C LEU 3.3 1.2 - - - -
99C GLY* 2.8 35.3 + - - -
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Residues in contact with LYS 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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135A ARG* 5.7 8.7 - - + -
65B ASN* 5.9 2.6 - - - +
92C GLU* 3.0 36.6 + - + +
93C GLU* 3.6 7.2 - - + +
95C ASN* 1.3 81.5 - - - +
97C LEU* 1.3 63.3 + - - +
99C GLY* 3.4 8.1 + - - -
104D PRO* 3.8 31.2 - - + +
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Residues in contact with LEU 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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59C LEU* 5.5 6.3 - - + -
93C GLU 3.0 16.5 + - - +
94C LEU* 3.7 17.5 - - + +
96C LYS* 1.3 78.1 - - - +
98C LEU* 1.3 69.2 + - + +
99C GLY 3.4 1.6 + - - -
100C ARG 5.4 0.2 + - - -
101C VAL* 4.6 0.3 - - - +
66D PHE* 4.3 15.9 - - + -
70D ILE* 4.2 22.2 - - + -
73D ARG* 3.5 35.6 + - - +
102D LEU* 4.4 15.0 - - + +
103D LEU* 4.4 28.9 - - + -
104D PRO* 5.5 6.6 - - + +
107D LEU* 5.4 4.9 - - + -
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Residues in contact with LEU 98 (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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63C ILE* 5.5 1.3 - - + -
88C ILE* 3.8 41.5 - - + -
89C ARG* 3.0 19.1 + - - +
94C LEU* 2.8 25.3 + - + +
95C ASN 3.3 3.8 - - - -
97C LEU* 1.3 90.1 - - + +
99C GLY* 1.3 61.0 + - - +
100C ARG 3.3 3.6 + - - -
101C VAL* 3.4 32.2 + - + +
103C ILE* 5.5 1.6 - - + -
66D PHE* 4.1 25.6 - - + -
69D ASP* 4.9 0.2 - - - +
70D ILE* 5.1 1.3 - - + -
73D ARG* 4.5 4.9 - - - +
99F TYR* 4.0 22.9 - - + +
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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