Contacts of the helix formed by residues 99 - 109 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95G VAL* 4.0 3.6 - - + -
96G LYS* 3.0 56.0 + - + +
97G ALA 4.2 2.7 - - - +
98G GLY* 1.3 84.2 - - - +
100G TYR* 1.3 55.6 + - - +
101G SER 3.4 2.5 - - - -
102G GLU* 3.0 22.7 + - + +
103G VAL* 2.6 39.0 + - + +
148G PRO* 4.1 18.2 - - - +
149G GLY* 3.7 23.2 - - - +
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Residues in contact with TYR 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G VAL* 3.8 24.7 + - + +
96G LYS 4.5 2.5 - - - -
97G ALA* 4.5 6.3 - - - -
98G GLY* 3.4 21.4 - - - -
99G LYS* 1.3 76.2 - - - +
101G SER* 1.3 59.1 + - - +
103G VAL* 4.7 0.2 - - - -
104G ALA* 2.9 33.1 + - - +
118G GLU* 3.5 41.5 - - + +
124G ASP* 3.3 49.4 + - + +
125G MET* 3.4 11.4 - - + +
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Residues in contact with SER 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G GLY 5.2 1.5 + - - -
99G LYS 3.4 0.2 - - - -
100G TYR* 1.3 79.6 - - - +
102G GLU* 1.3 55.6 + - - +
104G ALA* 3.7 4.6 + - - +
105G SER* 2.5 40.6 + - - -
162H HIS* 4.9 8.2 + - - -
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Residues in contact with GLU 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G GLY 5.2 3.3 + - - +
99G LYS* 3.0 32.1 + - + +
101G SER* 1.3 78.2 - - - +
103G VAL* 1.3 65.9 + - + +
105G SER* 3.4 6.5 + - - -
106G ASN* 3.0 23.4 + - - +
147G ILE* 5.6 0.7 - - - -
148G PRO 5.4 2.5 - - - +
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Residues in contact with VAL 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G VAL* 4.9 0.9 - - + -
95G VAL* 4.4 11.2 - - + -
99G LYS* 2.6 25.6 + - + +
100G TYR 4.0 2.5 - - - +
102G GLU* 1.3 72.5 - - - +
104G ALA* 1.3 51.0 - - - +
106G ASN* 3.2 3.8 + - - +
107G LEU* 2.8 54.4 + - + +
125G MET* 4.1 12.1 - - + -
147G ILE* 3.9 12.1 - - + -
148G PRO 3.5 24.2 - - - +
149G GLY* 3.8 22.4 - - - +
150G VAL* 3.9 16.8 - - + +
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Residues in contact with ALA 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G TYR 2.9 18.9 + - - +
101G SER 3.9 3.1 - - - +
103G VAL* 1.3 75.7 - - - +
105G SER* 1.3 52.3 + - - +
107G LEU* 3.3 8.3 + - - +
108G ALA* 2.7 38.1 + - - +
116G VAL* 4.5 4.8 - - + +
125G MET* 3.8 11.4 - - + +
162H HIS* 3.5 41.3 - - + +
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Residues in contact with SER 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G SER* 2.5 27.3 + - - -
102G GLU* 3.8 6.8 - - - -
103G VAL 3.4 0.2 - - - -
104G ALA* 1.3 72.5 - - - +
106G ASN* 1.3 66.5 + - - +
108G ALA* 4.0 6.5 - - - +
109G LYS* 3.3 41.5 + - - +
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Residues in contact with ASN 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G GLU 3.0 14.7 + - - +
103G VAL 3.4 8.5 - - - +
105G SER* 1.3 78.3 - - - +
107G LEU* 1.3 62.9 + - - +
109G LYS* 3.5 25.6 + - - +
110G TYR* 3.7 19.8 + - - -
147G ILE* 3.8 39.3 - - + +
148G PRO* 4.6 8.5 - - - +
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Residues in contact with LEU 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G VAL* 4.9 5.8 - - + -
103G VAL* 2.8 40.3 + - + +
104G ALA 3.6 3.4 - - - +
106G ASN* 1.3 73.1 - - - +
108G ALA* 1.3 57.9 + - - +
109G LYS 3.0 6.1 + - - -
110G TYR* 3.1 23.6 + - + +
113G ILE* 3.7 33.3 - - + +
116G VAL* 4.2 11.9 - - + -
125G MET* 4.0 14.1 - - - -
127G VAL* 3.9 24.2 - - + -
144G ILE* 3.8 22.0 - - + -
147G ILE* 3.7 22.9 - - + -
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Residues in contact with ALA 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G ALA 2.7 22.5 + - - +
105G SER* 4.0 7.9 - - - +
106G ASN 3.4 0.4 - - - -
107G LEU* 1.3 71.5 - - - +
109G LYS* 1.3 58.0 + - + +
110G TYR 3.3 0.4 - - - -
116G VAL* 4.6 2.9 - - + +
162H HIS* 5.1 6.5 - - + +
163H LYS* 2.8 52.7 + - + -
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Residues in contact with LYS 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G SER* 3.3 34.9 + - - +
106G ASN* 3.5 19.0 + - - +
107G LEU 3.0 1.2 + - - -
108G ALA* 1.3 76.3 - - + +
110G TYR* 1.3 66.8 + - + +
111G PRO* 3.4 9.2 - - - +
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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