Contacts of the helix formed by residues 95 - 102 (chain C) in PDB entry 1Y8Q
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 95 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C LEU* 4.5 3.5 - - - +
65C MET* 3.8 12.6 - - - -
79C GLN* 3.3 21.1 + - - -
81C LEU* 3.5 27.8 - - - +
82C ILE* 3.7 4.3 - - - +
91C ARG 2.8 19.5 + - - -
92C ALA* 3.0 10.1 + - - -
94C ALA* 1.3 81.7 - - - +
96C LEU* 1.3 65.3 + - - +
97C GLU 3.4 2.2 + - - -
98C ARG 3.5 2.3 + - - -
99C ALA* 3.1 22.3 + - - +
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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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65C MET* 3.9 5.6 - - - -
92C ALA 3.2 4.2 + - - -
93C GLU* 3.6 16.9 + - + +
95C SER* 1.3 76.4 - - - +
97C GLU* 1.3 57.5 + - - +
99C ALA* 3.2 2.1 + - - +
100C GLN* 2.9 57.0 + - + +
108C VAL* 3.3 34.5 - - + +
109C LYS* 4.4 1.6 - - - -
110C VAL* 3.7 35.4 - - + +
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Residues in contact with GLU 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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83C ARG* 2.9 46.9 + - + +
93C GLU 4.9 0.8 + - - -
94C ALA 5.2 2.6 + - - +
95C SER 3.4 0.6 - - - -
96C LEU* 1.3 80.1 - - - +
98C ARG* 1.3 72.8 + - + +
100C GLN* 3.2 11.2 + - - +
101C ASN* 3.0 40.0 + - - +
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Residues in contact with ARG 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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80C PHE 3.0 23.8 + - - -
81C LEU* 3.4 32.7 + - + +
82C ILE 2.9 23.3 + - - -
83C ARG* 3.4 27.2 - - + +
84C THR* 4.0 5.7 + - - +
95C SER 3.5 2.6 + - - -
97C GLU* 1.3 88.7 + - + +
99C ALA* 1.3 62.9 + - - +
101C ASN* 3.4 12.9 + - - +
102C LEU* 3.3 25.8 + - - +
82D GLN* 3.0 39.7 + - - +
83D PHE* 3.1 21.4 - - - +
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Residues in contact with ALA 99 (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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56C ILE* 3.6 32.7 - - + +
65C MET* 4.1 20.6 - - + -
81C LEU* 4.0 10.9 - - + +
95C SER 3.1 18.9 + - - +
96C LEU 3.6 4.5 - - - +
98C ARG* 1.3 76.0 - - - +
100C GLN* 1.3 63.4 + - - +
102C LEU* 3.3 26.7 + - - +
108C VAL* 4.2 5.6 - - + -
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Residues in contact with GLN 100 (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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96C LEU* 2.9 45.6 + - + +
97C GLU* 3.6 9.6 - - - +
99C ALA* 1.3 76.8 - - - +
101C ASN* 1.3 63.8 + - - +
102C LEU 3.1 1.4 + - - -
103C ASN 3.2 23.1 + - - +
104C PRO* 3.8 5.0 - - - +
106C VAL 5.5 2.5 - - - +
108C VAL* 3.3 38.4 + - + +
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Residues in contact with ASN 101 (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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97C GLU* 3.0 37.9 + - - +
98C ARG* 3.8 11.4 - - - +
99C ALA 3.3 0.4 - - - -
100C GLN* 1.3 78.6 - - - +
102C LEU* 1.3 61.2 + - + +
103C ASN* 3.2 1.4 + - - -
104C PRO* 4.4 10.1 - - - +
64D GLN* 3.2 32.0 - - + +
66D LYS* 6.0 2.0 - - - +
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Residues in contact with LEU 102 (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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53C LYS* 3.7 37.0 - - + +
56C ILE* 4.0 11.2 - - + -
57C LEU* 3.8 20.0 - - + +
81C LEU* 4.0 16.8 - - + -
98C ARG 3.3 15.9 - - - +
99C ALA* 3.5 13.0 - - - +
100C GLN 3.1 1.0 + - - -
101C ASN* 1.3 77.5 - - - +
103C ASN* 1.3 62.6 + - - +
104C PRO* 4.4 1.0 - - - +
57D LEU 4.7 3.5 - - - +
61D PHE* 3.7 46.9 - - + +
63D PHE 5.5 1.0 - - - +
64D GLN* 4.4 10.0 + - - +
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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