Contacts of the helix formed by residues 97 - 105 (chain D) in PDB entry 5COX
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 LYS 97 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D HIS 2.8 7.7 + - - -
96D PHE* 1.3 69.0 - - - +
98D GLY* 1.3 57.1 + - - +
100D TRP* 3.7 4.0 - - - +
101D ASN* 3.0 26.5 + - - +
104D ASN* 5.3 2.2 - - - +
356D HIS* 3.2 66.7 + - + +
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Residues in contact with GLY 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D PHE 2.6 6.1 + - - -
97D LYS* 1.3 74.7 - - - +
99D VAL* 1.3 66.8 + - - +
100D TRP 3.1 0.7 - - - -
101D ASN* 3.0 15.2 + - - +
102D ILE* 3.1 18.5 + - - +
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Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D PHE* 2.6 39.5 + - + +
98D GLY* 1.3 69.9 - - - +
100D TRP* 1.3 61.8 + - + +
102D ILE* 2.9 39.5 + - + +
103D VAL* 3.3 15.0 + - + +
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Residues in contact with TRP 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ILE* 2.9 30.4 + - + -
93D LEU* 3.1 39.4 + - + -
95D HIS 2.8 27.1 - - - -
96D PHE* 2.9 14.0 + + + +
97D LYS 3.7 9.2 - - - +
99D VAL* 1.3 81.9 - - + +
101D ASN* 1.3 56.1 + - - +
103D VAL* 3.3 27.0 - - + +
104D ASN* 3.0 32.1 + - - +
112D ILE* 4.4 16.8 - - + -
356D HIS* 3.8 21.1 - - + +
357D PHE* 3.5 38.8 - + + -
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Residues in contact with ASN 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LYS* 3.0 21.0 + - + +
98D GLY* 3.0 11.2 + - - +
100D TRP* 1.3 72.8 - - - +
102D ILE* 1.3 69.5 + - - +
104D ASN* 3.4 16.8 + - - +
105D ASN* 3.0 38.9 + - - +
358D LYS* 5.8 0.2 + - - -
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Residues in contact with ILE 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D GLY 3.1 15.3 + - - +
99D VAL* 2.9 18.4 + - + +
101D ASN* 1.3 78.7 - - - +
103D VAL* 1.3 66.7 + - + +
105D ASN* 2.9 50.3 + - - +
108D LEU* 5.3 2.2 - - + -
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Residues in contact with VAL 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D VAL* 3.5 21.1 - - + +
100D TRP* 3.3 33.2 - - + +
102D ILE* 1.3 73.0 - - + +
104D ASN* 1.3 54.1 + - - +
105D ASN 2.5 40.7 + - - +
108D LEU* 4.5 20.2 - - + -
109D ARG* 4.1 8.1 - - - +
112D ILE* 3.8 31.4 - - + -
357D PHE* 4.0 10.5 - - + -
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Residues in contact with ASN 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LYS* 5.3 2.8 - - - +
100D TRP 3.0 15.2 + - - +
101D ASN* 3.6 17.7 + - - +
102D ILE 3.3 0.2 - - - -
103D VAL* 1.3 72.4 - - - +
105D ASN* 1.3 62.2 + - - +
106D PRO* 5.6 0.4 - - - -
109D ARG* 4.7 14.2 + - - +
356D HIS 2.9 25.2 + - - -
357D PHE* 3.4 14.0 - - - -
358D LYS* 2.9 69.7 + - - +
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Residues in contact with ASN 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ASN* 3.0 33.5 + - - +
102D ILE* 2.9 11.6 + - - +
103D VAL 2.5 7.3 + - - -
104D ASN* 1.3 80.9 - - - +
105D ILE* 1.3 60.2 + - - +
106D PRO* 3.1 14.3 - - - +
358D LYS* 4.9 2.6 + - - -
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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