Contacts of the helix formed by residues 57 - 65 (chain B) in PDB entry 4ZIN
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 ALA 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B PHE* 1.3 85.2 - - - +
58B TRP* 1.3 67.7 + - - +
59B ASP* 3.1 5.1 + - + +
60B ILE* 3.3 13.5 + - + +
134B PRO 4.4 3.4 - - - +
135B VAL* 2.9 32.4 + - + +
138B LYS* 3.9 13.0 - - - +
140B THR* 3.6 25.6 - - + +
165B LEU* 6.2 0.2 - - + -
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Residues in contact with TRP 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 3.9 31.6 - - + -
46B LEU* 4.0 23.3 - - + -
48B VAL* 4.0 10.1 - - + -
54B LEU* 4.3 8.1 - - + -
56B PHE* 3.3 5.8 + - - -
57B ALA* 1.3 72.4 - - - +
59B ASP* 1.3 59.6 + - - +
61B LEU* 2.8 37.8 + - + +
62B SER* 3.3 6.7 + - - -
65B PHE* 3.9 15.9 - + - -
201B ILE* 3.9 20.2 - - + +
208B TYR* 3.8 46.8 - + + -
211B VAL* 3.8 32.3 - - + +
213B GLN* 2.8 28.8 + - - -
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Residues in contact with ASP 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA* 3.1 2.6 - - + -
58B TRP* 1.3 78.8 - - - +
60B ILE* 1.3 59.9 + - - +
62B SER* 2.8 25.8 + - - -
63B PRO* 3.2 0.7 - - - +
140B THR* 2.4 31.3 + - - +
141B MET* 3.6 1.7 + - - -
142B GLY* 2.9 34.7 + - - -
143B 4OO 3.0 18.5 + - + -
165B LEU* 3.6 24.9 - - + -
201B ILE* 4.4 15.2 - - - +
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Residues in contact with ILE 60 (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 VAL* 3.8 36.8 - - + -
56B PHE* 4.0 11.4 - - + -
57B ALA* 3.3 17.6 + - + +
58B TRP 2.9 0.6 + - - -
59B ASP* 1.3 77.6 - - - +
61B LEU* 1.3 65.6 + - + +
63B PRO* 3.8 2.3 - - - +
64B GLN* 3.2 23.2 + - - +
97B MET* 4.7 2.9 - - - +
99B PHE* 3.8 29.6 - - + -
105B VAL* 4.5 10.3 - - + +
124B LEU* 4.4 3.2 - - + +
129B PHE* 4.4 10.1 - - + -
135B VAL* 3.9 31.2 - - + -
143B 4OO 4.2 5.1 + - - -
165B LEU* 4.8 6.3 - - + -
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Residues in contact with LEU 61 (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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18B MET* 4.2 3.4 - - + -
27B PHE* 3.7 26.2 - - + -
29B ILE* 3.5 29.6 - - + -
54B LEU* 3.8 18.6 - - + -
56B PHE* 3.9 19.1 - - + -
58B TRP* 2.8 20.4 + - + +
60B ILE* 1.3 80.2 - - + +
62B SER* 1.3 64.5 + - - +
63B PRO* 3.3 4.5 - - - -
64B GLN* 3.0 21.2 + - - +
65B PHE* 3.3 25.3 - - + -
124B LEU* 3.9 24.2 - - + -
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Residues in contact with SER 62 (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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58B TRP* 3.3 17.2 + - - +
59B ASP* 2.8 25.0 + - - -
61B LEU* 1.3 77.0 - - - +
63B PRO* 1.3 62.5 - - - +
64B GLN 3.1 4.7 + - - -
65B PHE* 3.5 7.9 + - - -
66B CH6 3.7 4.3 - - - +
143B 4OO 3.2 13.5 - - - -
199B LEU* 3.2 17.6 - - - +
201B ILE* 4.2 5.8 - - - -
213B GLN* 3.1 42.3 + - - -
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Residues in contact with PRO 63 (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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59B ASP 3.2 7.9 - - - +
60B ILE 3.8 6.1 - - - +
61B LEU 3.3 5.2 - - - -
62B SER* 1.3 95.6 - - - +
64B GLN* 1.3 62.7 + - - +
65B PHE 3.4 1.1 - - - -
66B CH6 2.8 70.7 + - + +
95B ARG* 3.2 9.8 + - - +
97B MET* 4.7 1.1 - - + -
143B 4OO 3.4 37.0 - - + +
163B GLN* 4.5 2.2 - - - +
199B LEU* 4.4 1.1 - - + -
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Residues in contact with GLN 64 (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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18B MET* 3.6 15.9 - - + -
60B ILE 3.2 18.6 + - - -
61B LEU 3.0 15.5 + - - +
63B PRO* 1.3 79.0 - - - +
65B PHE* 1.3 64.0 + - - +
66B CH6 3.7 12.9 - - - +
93B TRP* 3.5 16.5 - - + -
95B ARG* 2.8 31.8 + - - +
97B MET* 3.3 30.7 - - - +
107B VAL* 3.7 14.0 - - + +
122B VAL* 3.9 23.3 - - + +
124B LEU* 3.7 22.4 - - + +
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Residues in contact with PHE 65 (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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14B PHE* 4.8 8.6 - - + -
16B VAL* 3.9 33.7 - - + -
18B MET* 3.5 42.6 - - + -
29B ILE* 4.0 28.3 - - + -
42B GLN* 4.2 2.3 - - - +
44B ALA* 5.5 2.9 - - + -
46B LEU* 4.2 15.7 - - + -
58B TRP* 3.9 17.7 - + - -
61B LEU* 3.3 26.9 - - + -
62B SER* 3.5 10.9 + - - +
63B PRO 3.4 0.8 - - - -
64B GLN* 1.3 80.4 - - - +
66B CH6 1.3 71.7 + - + +
69B SER* 3.0 10.3 + - - -
120B TYR* 5.3 5.8 - - - -
122B VAL* 5.0 0.9 - - + -
213B GLN* 4.0 14.8 - - - +
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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
------------------------------------------------------------
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