Contacts of the helix formed by residues 91 - 98 (chain S) in PDB entry 6Y5D
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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236L ARG* 5.4 1.0 + - - -
255L ARG* 2.9 38.6 + - - -
257L PRO* 4.9 8.4 - - - +
66S LEU* 3.5 31.6 - - + +
87S ALA 3.8 5.8 - - - +
88S ILE 3.1 3.5 + - - +
89S ARG 3.3 1.4 - - - -
90S ASN* 1.3 80.6 - - - +
92S GLU* 1.3 60.8 + - - +
93S GLU 3.2 5.4 + - - -
94S LEU* 3.1 22.3 + - + +
95S ASN* 2.7 31.3 + - - +
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Residues in contact with GLU 92 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257L PRO* 3.0 31.8 - - + +
258L LYS* 4.0 25.9 + - - +
89S ARG 5.9 0.2 - - - -
90S ASN 4.6 4.5 - - - +
91S ASP* 1.3 77.1 + - - +
93S GLU* 1.3 59.6 + - + +
95S ASN* 3.7 11.5 + - - +
96S LYS* 2.8 30.8 + - - +
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Residues in contact with GLU 93 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255L ARG* 2.7 46.5 + - - +
257L PRO* 4.4 19.9 - - + +
91S ASP* 3.2 2.4 + - - -
92S GLU* 1.3 76.3 - - + +
94S LEU* 1.3 62.2 + - - +
96S LYS* 3.4 5.7 + - - +
97S LEU* 3.0 23.6 + - - +
104T PRO* 3.5 22.0 - - + +
105T GLY* 3.6 6.3 - - - -
106T GLU* 2.9 34.4 + - - +
107T LEU* 3.6 17.5 + - + -
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Residues in contact with LEU 94 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255L ARG* 5.0 0.2 - - - +
59S LEU* 4.5 11.0 - - + +
62S GLU* 4.1 15.9 - - + -
63S ILE* 4.0 34.5 - - + +
66S LEU* 3.5 32.5 - - + -
87S ALA 4.8 2.7 - - - +
88S ILE* 4.0 16.8 - - + +
91S ASP* 3.1 16.7 + - + +
93S GLU* 1.3 73.0 - - - +
95S ASN* 1.3 61.3 + - - +
97S LEU* 3.0 11.3 + - + +
98S LEU* 2.8 34.8 + - + +
66T PHE* 6.0 0.2 - - + -
107T LEU* 3.8 28.7 - - + -
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Residues in contact with ASN 95 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88S ILE* 3.3 18.1 + - - +
89S ARG* 3.0 41.6 + - - +
91S ASP 2.7 25.6 + - - +
92S GLU* 3.7 10.3 + - - +
94S LEU* 1.3 72.4 - - - +
96S LYS* 1.3 53.7 - - - +
98S LEU 3.3 0.2 - - - -
99S GLY* 2.7 42.0 + - - -
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Residues in contact with LYS 96 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134Q GLU* 6.1 5.9 - - - +
65R ASN* 6.1 0.6 - - - +
92S GLU 2.8 19.4 + - - +
93S GLU* 3.5 7.2 - - - +
95S ASN* 1.3 78.4 - - - +
97S LEU* 1.3 62.9 + - - +
98S LEU 3.2 0.9 + - - -
99S GLY* 3.2 11.0 + - - -
100S LYS* 6.0 0.5 - - - +
104T PRO* 4.0 20.6 - - + -
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Residues in contact with LEU 97 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59S LEU* 3.9 37.2 - - + -
93S GLU 3.0 14.1 + - - +
94S LEU* 3.0 14.5 + - + +
96S LYS* 1.3 76.4 - - - +
98S LEU* 1.3 71.6 + - + +
99S GLY 3.9 0.5 + - - -
66T PHE* 5.2 1.8 - - + -
70T ILE* 4.3 10.5 - - + -
73T ARG* 3.4 34.3 + - - +
102T LEU* 3.4 30.7 - - + +
103T LEU* 4.3 13.0 - - + -
104T PRO* 4.3 7.4 - - + +
107T LEU* 4.5 5.2 - - + -
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Residues in contact with LEU 98 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99N TYR* 3.7 27.4 - - + +
63S ILE* 4.0 8.5 - - + -
88S ILE* 3.9 36.6 - - + -
89S ARG* 3.3 13.2 + - - +
94S LEU* 2.8 16.8 + - + +
95S ASN 3.3 3.1 - - - -
97S LEU* 1.3 95.6 - - + +
99S GLY* 1.3 55.7 + - - +
100S LYS 2.9 11.9 + - - -
101S VAL* 3.0 28.5 + - + +
66T PHE* 3.9 29.2 - - + -
69T ASP* 4.9 0.4 - - - +
70T ILE* 4.4 6.5 - - + -
73T ARG* 4.8 3.6 - - - +
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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