Contacts of the helix formed by residues 98 - 106 (chain B) in PDB entry 2ZZA
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 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B THR* 3.1 11.2 + - - -
97B GLY* 1.3 70.6 + - - -
99B ALA* 1.3 68.7 + - - -
100B THR 3.2 2.5 - - - -
101B ILE* 3.2 1.6 + - - +
102B TYR* 3.0 28.4 + - - -
163B NAP 3.0 37.5 + - - -
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 4.1 4.4 - - + +
98B GLY* 1.3 74.0 - - - +
100B THR* 1.3 57.4 + - + +
102B TYR* 3.2 10.2 + - - +
103B ASN* 2.8 39.8 + - - +
125B THR* 4.2 22.2 - - + -
126B TRP 3.6 23.8 - - - +
163B NAP 2.7 18.2 + - - +
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Residues in contact with THR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ASN* 5.5 0.7 - - - +
99B ALA* 1.3 79.1 - - + +
101B ILE* 1.3 74.1 + - - +
103B ASN* 3.5 9.4 - - - +
104B GLN* 3.0 34.9 + - - +
163B NAP 2.9 54.3 + - - +
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Residues in contact with ILE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B MET* 4.6 0.2 - - - -
42B VAL* 4.8 7.0 - - + +
44B GLY* 3.6 24.5 - - - +
63B LEU* 3.6 33.4 - - + -
80B LEU* 4.4 2.7 - - + -
95B ILE* 3.7 21.8 - - + -
97B GLY* 3.7 8.1 - - - +
98B GLY 3.2 4.4 + - - +
100B THR* 1.3 83.8 - - - +
102B TYR* 1.3 69.1 + - - +
104B GLN* 3.2 5.4 + - - +
105B CYS* 2.9 34.8 + - - -
163B NAP 3.6 33.7 - - + +
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Residues in contact with TYR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B MET* 2.9 37.5 - - + +
6B ILE 2.6 30.5 + - - -
7B ALA* 3.2 8.9 - - + +
15B ILE* 3.7 25.6 - - + -
95B ILE* 3.8 7.4 - - + -
96B ILE 3.1 11.8 + - - -
97B GLY* 3.2 29.4 - - - -
98B GLY* 3.0 21.7 + - - -
99B ALA* 3.5 4.7 - - - +
101B ILE* 1.3 76.6 - - - +
103B ASN* 1.3 54.9 + - - +
106B LEU* 2.8 37.6 + - - +
127B PHE* 3.6 23.8 - + - -
128B PRO* 3.4 19.5 - - + +
163B NAP 3.2 13.7 - + - -
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Residues in contact with ASN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ALA* 2.8 26.6 + - - +
100B THR* 3.5 9.7 - - - +
101B ILE 3.1 0.2 - - - -
102B TYR* 1.3 77.7 - - - +
104B GLN* 1.3 63.8 + - + +
106B LEU* 3.7 9.9 + - - +
107B ALA* 4.9 1.6 + - - +
126B TRP 4.6 4.6 + - - -
128B PRO* 3.4 34.3 - - - +
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ARG* 5.7 1.0 - - - +
80B LEU* 3.7 25.8 - - + +
100B THR* 3.0 25.3 + - - +
101B ILE* 3.2 7.7 + - - +
103B ASN* 1.3 81.8 - - + +
105B CYS* 1.3 61.3 + - - +
107B ALA* 4.8 5.2 + - - +
108B ALA* 5.3 2.1 + - - +
163B NAP 2.8 48.5 + - - -
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Residues in contact with CYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B VAL* 5.1 2.5 - - + -
5B MET* 3.6 8.3 - - - -
80B LEU* 4.0 31.4 - - - -
95B ILE* 3.4 35.7 - - + -
101B ILE* 2.9 23.8 + - - +
104B GLN* 1.3 79.5 - - - +
106B LEU* 1.3 64.2 + - - +
107B ALA 3.3 2.9 - - - -
108B ALA* 2.9 20.1 + - + +
109B ALA* 3.0 11.4 + - - +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B MET* 3.8 6.7 - - - -
102B TYR 2.8 21.4 + - - +
103B ASN 3.7 7.4 + - - +
104B GLN 3.6 1.0 - - - -
105B CYS* 1.3 71.4 - - - +
107B ALA* 1.3 65.0 + - - +
109B ALA* 3.0 17.5 + - - +
112B LEU* 4.4 12.6 - - + -
127B PHE* 5.0 1.6 - - + -
128B PRO* 3.6 31.6 - - + -
129B ASP 4.2 4.3 - - - +
130B TYR* 3.8 37.2 - - + +
132B GLN* 4.4 4.9 - - - +
133B TYR* 3.7 19.7 - - + -
135B TRP* 4.0 16.2 - - + -
160B ARG* 3.4 8.5 + - - -
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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