Contacts of the helix formed by residues 47 - 52 (chain B) in PDB entry 2Z9I
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 ASN 47 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B THR* 1.3 81.0 + - - +
48B ASN* 1.3 66.5 + - - +
49B HIS* 3.4 16.8 - - + +
50B VAL* 3.4 16.4 + - + +
51B ILE* 3.5 13.9 - - - +
88B ASP* 2.8 30.3 + - - +
89B ILE* 4.0 0.2 - - - +
90B ALA* 4.0 1.8 - - - -
169B SER* 3.4 7.8 - - - -
170B GLY* 3.1 23.8 + - - -
183B VAL* 3.8 10.5 - - - +
184B ASN 3.2 8.1 - - - +
185B SER* 2.9 31.3 + - - -
208B ILE* 3.8 3.4 - - - +
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Residues in contact with ASN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASN* 1.3 72.0 - - - +
49B HIS* 1.3 63.7 + - - +
51B ILE* 3.1 5.9 + - - +
52B ALA* 2.9 34.7 + - - +
83B ALA* 3.1 28.2 - - - +
84B ASP 3.8 9.6 + - - +
85B PRO* 3.6 33.0 + - - +
88B ASP* 3.1 18.7 + - - +
89B ILE 3.7 16.1 - - - +
90B ALA* 3.7 9.4 - - - -
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Residues in contact with HIS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLU* 3.4 17.5 - - - +
47B ASN* 3.2 26.0 - - + +
48B ASN* 1.3 76.9 - - - +
50B VAL* 1.3 64.7 + - + +
51B ILE 3.5 0.2 + - - -
52B ALA* 3.9 9.7 - - + +
88B ASP* 2.8 38.8 + - - +
169B SER* 3.2 28.2 + - - -
185B SER 3.7 4.0 - - - -
410E GLN* 3.5 35.2 + - + +
411E VAL* 3.2 10.5 + - - -
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Residues in contact with VAL 50 (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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22B LEU* 4.0 19.6 - - + +
24B THR* 4.1 4.5 + - - -
31B GLU* 3.1 27.4 - - - +
32B GLU 4.6 2.2 - - - +
33B GLY* 3.8 29.4 - - - +
34B SER 4.1 1.1 - - - +
46B THR* 3.8 12.3 - - - +
47B ASN* 3.7 17.7 - - + +
48B ASN 3.2 1.0 - - - -
49B HIS* 1.3 81.4 - - + +
51B ILE* 1.3 59.3 + - + +
169B SER* 3.0 43.3 - - - +
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Residues in contact with ILE 51 (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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22B LEU* 3.9 22.9 - - + -
24B THR* 4.9 3.1 - - - -
31B GLU* 3.6 1.1 - - - -
46B THR* 3.8 12.8 - - + -
47B ASN 3.5 15.3 - - - +
48B ASN* 3.7 5.8 - - - +
50B VAL* 1.3 80.5 - - + +
52B ALA* 1.3 52.7 + - - +
53B ALA 2.7 17.7 + - - +
54B ALA* 3.0 17.7 + - - +
78B PHE* 3.6 36.1 - - + -
80B VAL* 4.2 19.1 - - + -
83B ALA* 4.2 14.1 - - + -
90B ALA* 3.6 20.4 - - + -
92B VAL* 4.1 5.4 - - + -
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Residues in contact with ALA 52 (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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31B GLU* 3.0 8.8 + - - +
48B ASN* 2.9 22.9 + - - +
49B HIS* 3.9 16.2 - - + +
51B ILE* 1.3 73.5 - - - +
53B ALA* 1.3 57.1 + - - +
54B ALA 3.6 2.8 + - - -
55B ALA* 4.3 16.5 + - - +
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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