Contacts of the helix formed by residues 99 - 109 (chain C) in PDB entry 2ZNZ
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 99 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95C VAL* 3.5 9.8 - - + +
96C LYS 3.0 15.7 + - - +
97C ALA* 3.5 21.3 + - + +
98C GLY* 1.3 73.4 - - - +
100C TYR* 1.3 63.0 + - - +
101C SER 3.3 2.2 - - - -
102C GLU* 3.2 35.3 + - + +
103C VAL* 3.1 21.1 + - + +
148C PRO 5.2 1.8 - - - +
149C GLY* 4.1 20.6 - - - -
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Residues in contact with TYR 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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94C LYS* 5.1 3.5 + - - -
95C VAL* 3.7 24.3 + - + +
98C GLY* 2.8 43.2 + - - +
99C LYS* 1.3 72.4 - - - +
101C SER* 1.3 62.3 + - - +
104C ALA* 3.3 8.8 + - - +
118C GLU* 3.8 26.7 - - + +
124C ASP* 3.7 37.6 + - + -
125C MET* 3.1 28.1 - - + +
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Residues in contact with SER 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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98C GLY 4.8 0.4 + - - -
99C LYS 3.3 0.4 - - - -
100C TYR* 1.3 78.9 - - - +
102C GLU* 1.3 63.8 + - - +
104C ALA* 3.4 6.2 + - - +
105C SER* 2.7 33.1 + - - -
118C GLU* 4.6 3.1 + - - -
160D LYS* 5.5 5.9 + - - +
162D HIS* 5.1 4.8 + - - -
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Residues in contact with GLU 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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98C GLY 4.6 1.2 - - - +
99C LYS* 3.2 49.3 + - + +
101C SER* 1.3 85.2 + - - +
103C VAL* 1.3 62.1 + - + +
105C SER* 3.5 7.9 + - - -
106C ASN* 3.4 20.4 + - - +
147C ILE* 5.3 1.1 - - - +
148C PRO 5.3 5.2 - - - +
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Residues in contact with VAL 103 (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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93C VAL* 4.6 1.6 - - + -
95C VAL* 4.0 15.7 - - + -
99C LYS* 3.1 17.1 + - + +
100C TYR 4.2 2.0 - - - +
102C GLU* 1.3 73.5 - - - +
104C ALA* 1.3 63.7 + - - +
106C ASN* 3.2 5.0 + - - +
107C LEU* 3.0 41.8 + - + +
125C MET* 3.8 11.0 - - - -
147C ILE* 4.4 8.3 - - + -
148C PRO 4.1 4.9 - - - +
149C GLY* 3.5 39.5 - - - +
150C VAL* 3.8 20.6 - - + +
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Residues in contact with ALA 104 (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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100C TYR 3.3 14.7 + - - +
101C SER 3.7 3.1 - - - +
103C VAL* 1.3 79.2 - - - +
105C SER* 1.3 57.7 + - - +
107C LEU* 3.5 5.5 + - - +
108C ALA* 3.1 30.0 + - - +
116C VAL* 4.5 6.0 - - + +
125C MET* 3.7 12.5 - - + +
162D HIS* 3.4 48.0 - - + +
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Residues in contact with SER 105 (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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101C SER* 2.7 19.3 + - - -
102C GLU* 3.8 7.7 + - - -
103C VAL 3.3 0.6 - - - -
104C ALA* 1.3 74.4 - - - +
106C ASN* 1.3 63.5 + - - +
107C LEU 3.7 0.2 + - - -
108C ALA* 3.8 5.1 + - - +
109C LYS* 3.3 30.9 + - - +
162D HIS* 5.8 1.3 - - - -
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Residues in contact with ASN 106 (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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102C GLU 3.4 10.3 + - - +
103C VAL 3.2 9.1 + - - +
105C SER* 1.3 79.7 - - - +
107C LEU* 1.3 62.8 + - - +
109C LYS* 3.6 23.4 + - - +
110C TYR* 3.5 23.3 + - - -
147C ILE* 3.5 44.5 - - + +
148C PRO* 4.7 6.3 - - - +
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Residues in contact with LEU 107 (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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93C VAL* 4.7 5.8 - - + -
103C VAL* 3.0 39.4 + - + +
104C ALA 3.9 3.1 - - - +
105C SER 3.4 0.2 - - - -
106C ASN* 1.3 73.2 - - - +
108C ALA* 1.3 64.9 + - - +
109C LYS 3.1 3.9 + - - -
110C TYR* 3.2 14.6 + - + -
113C ILE* 3.3 33.3 - - + +
116C VAL* 4.2 13.0 - - + -
125C MET* 3.9 14.6 - - - -
127C VAL* 3.8 24.0 - - + -
144C ILE* 3.8 37.5 - - + -
147C ILE* 3.8 13.9 - - + -
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Residues in contact with ALA 108 (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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104C ALA 3.1 16.3 + - - +
105C SER* 4.2 6.7 - - - +
106C ASN 3.5 0.4 - - - -
107C LEU* 1.3 77.7 - - - +
109C LYS* 1.3 58.2 + - + +
110C TYR 3.3 0.4 - - - -
116C VAL* 4.3 5.6 - - + +
162D HIS* 5.0 6.7 - - + +
163D LYS* 2.9 55.5 + - + +
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Residues in contact with LYS 109 (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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105C SER* 3.3 22.0 - - - +
106C ASN* 3.7 21.2 - - - +
107C LEU 3.1 1.0 - - - -
108C ALA* 1.3 77.7 - - + +
110C TYR* 1.3 63.5 + - + +
111C PRO* 3.4 9.5 - - - +
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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