Contacts of the helix formed by residues 99 - 103 (chain A) in PDB entry 3N9Z
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A PRO 4.2 0.4 + - - -
98A ILE* 1.3 73.3 - - - +
100A VAL* 1.3 66.4 + - - -
101A LEU 3.2 3.1 - - - -
102A LEU* 3.1 11.6 + - - -
103A LYS* 3.3 19.5 + - - +
111A ASP* 4.3 0.9 - - - -
279A ALA* 4.0 7.1 + - - +
280A ASN* 3.4 18.8 - - - -
283A GLU* 3.0 21.8 + - - -
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A GLY* 1.3 72.0 - - - -
101A LEU* 1.3 62.7 + - - +
102A LEU 3.2 0.7 + - - -
103A LYS* 3.4 7.1 + - - -
108A TRP* 3.2 53.5 - - + +
111A ASP* 4.1 8.2 + - + -
112A ARG* 4.0 19.5 - - + +
115A LEU* 4.2 4.3 - - + -
280A ASN* 2.8 20.9 + - - +
283A GLU* 3.2 1.7 + - - +
421A ARG* 2.9 22.3 + - - -
424A LEU* 4.0 15.0 - - + -
601A HEM 3.6 35.2 - - + +
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ARG* 3.7 22.5 + - - +
83A LEU* 3.8 12.7 - - + +
87A TRP* 3.7 33.0 - - + -
100A VAL* 1.3 80.6 - - - +
102A LEU* 1.3 69.3 + - + +
231A TRP* 5.7 3.4 - - + -
283A GLU* 3.1 20.7 + - + +
421A ARG* 3.3 11.6 + - - -
601A HEM 3.9 25.6 - - + -
602A HC9 3.8 43.7 - - + -
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 4.0 29.3 - - + +
84A ILE 5.5 1.8 - - - +
87A TRP* 4.4 16.6 - - + +
88A VAL* 4.2 19.7 - - + -
91A HIS* 3.4 47.3 - - + +
98A ILE* 3.8 30.5 - - + +
99A GLY 3.1 4.0 + - - +
101A LEU* 1.3 99.2 - - + +
103A LYS* 1.3 63.5 + - - +
104A LYS* 5.6 0.9 - - - +
283A GLU* 4.4 6.5 - - - +
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Residues in contact with LYS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 5.5 1.7 - - - +
98A ILE* 3.4 40.7 + - + -
99A GLY 3.3 13.2 + - - +
100A VAL* 3.4 4.5 + - - +
102A LEU* 1.3 80.5 - - - +
104A LYS* 1.3 62.4 + - - +
107A ALA* 3.7 28.3 + - + +
108A TRP* 3.8 18.2 - - + +
111A ASP* 2.8 33.2 + - + +
276A ASP* 3.0 26.2 + - - +
421A ARG* 2.8 26.3 + - - -
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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