Contacts of the helix formed by residues 84 - 90 (chain X) in PDB entry 1ZV4
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 84 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80X SER* 2.7 27.3 + - - +
81X TRP* 2.9 14.1 + - - +
82X SER 3.2 0.4 - - - -
83X GLN* 1.3 94.2 + - - +
85X PHE* 1.3 65.7 + - - +
86X ASP* 3.2 12.3 - - - +
87X LYS* 3.1 39.5 + - + +
88X MET 3.1 17.0 + - - -
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Residues in contact with PHE 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81X TRP 3.7 1.4 + - - -
84X ASN* 1.3 72.7 - - - +
86X ASP* 1.3 53.4 + - - +
88X MET* 3.2 14.3 + - + +
89X MET* 2.8 63.7 + - + +
98X PHE* 3.8 17.9 - + - -
179X TYR* 3.6 55.4 - + - +
182X MET* 3.9 12.6 - - + -
183X HIS* 3.3 41.7 + + + +
187X PHE* 3.3 44.3 - + + -
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Residues in contact with ASP 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84X ASN* 3.6 19.8 - - - +
85X PHE* 1.3 72.4 + - - +
87X LYS* 1.3 75.0 + - - +
89X MET* 3.5 5.8 + - - +
90X LYS* 3.2 32.5 + - + +
179X TYR* 3.3 21.3 + - + +
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Residues in contact with LYS 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77X GLU* 5.2 0.7 - - - +
80X SER* 3.8 28.0 - - - +
81X TRP* 4.2 5.9 + - + +
84X ASN* 3.1 43.1 + - + +
86X ASP* 1.3 84.2 - - - +
88X MET* 1.3 63.2 + - - +
90X LYS* 3.3 16.2 + - - +
91X ALA* 3.4 13.7 + - - +
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Residues in contact with MET 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81X TRP* 3.7 40.1 - - + +
84X ASN 3.1 9.6 + - - +
85X PHE* 3.5 26.2 - - + +
87X LYS* 1.3 77.5 - - - +
89X MET* 1.3 64.2 + - - +
90X LYS 3.1 0.2 - - - -
91X ALA* 3.1 21.7 + - - +
94X GLY* 3.5 23.4 - - - +
95X ARG 3.5 4.0 + - - -
98X PHE* 3.8 24.7 - - + -
187X PHE* 3.5 29.8 - - + -
190X PHE* 3.7 22.7 - - + -
191X LEU* 5.8 0.4 - - - -
196X TYR* 5.9 0.7 - - - -
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Residues in contact with MET 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85X PHE* 2.8 59.0 + - + +
86X ASP* 3.9 7.2 - - - +
88X MET* 1.3 74.2 - - - +
90X LYS* 1.3 59.1 + - + +
91X ALA 3.5 0.2 - - - -
95X ARG* 3.1 33.7 + - - -
98X PHE* 4.1 9.9 - - - -
111X LEU* 3.3 35.2 - - + -
114X TRP* 3.6 45.1 - - + +
179X TYR* 4.2 4.9 - - + -
182X MET* 3.8 17.0 - - + -
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Residues in contact with LYS 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86X ASP* 3.2 20.8 + - + +
87X LYS* 3.7 8.1 - - - +
88X MET 3.1 1.2 - - - -
89X MET* 1.3 78.6 - - + +
91X ALA* 1.3 57.6 + - - +
92X PRO* 3.6 8.0 - - - +
95X ARG* 3.7 10.4 + - - +
114X TRP* 5.5 4.7 - - + -
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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