Contacts of the strand formed by residues 6 - 11 (chain E) in PDB entry 3ZP0
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 GLN 6 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5E ASP* 1.3 75.9 - - - +
7E ILE* 1.3 60.7 + - - +
8E CYS* 4.1 5.8 - - - -
25F HIS 4.5 0.2 - - - -
26F HIS* 3.4 2.8 - - - -
27F SER* 2.9 46.5 + - - +
133F LEU* 3.9 18.8 - - + +
137F CYS* 4.0 23.9 - - + +
138F PHE 3.3 19.7 - - - +
139F GLU* 4.4 15.3 + - - +
140F PHE* 4.2 4.6 - - - -
149F MET* 3.9 3.6 - - - +
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Residues in contact with ILE 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E GLN* 1.3 74.8 - - - +
8E CYS* 1.3 70.4 + - - +
9E ILE* 6.1 0.4 - - + -
24F TYR* 4.2 22.9 - - + -
25F HIS 3.3 12.6 - - - +
26F HIS* 4.4 3.6 - - + -
122F VAL* 4.7 3.4 - - + -
126F LEU* 4.3 15.0 - - + -
137F CYS* 3.4 0.3 - - - -
138F PHE* 2.8 41.0 + - + -
140F PHE* 3.6 25.3 - - + -
149F MET* 4.0 24.2 - - + +
152F VAL* 4.0 29.8 - - + -
153F ARG* 4.4 6.5 - - + -
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Residues in contact with CYS 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E GLN* 4.1 12.8 - - - -
7E ILE* 1.3 77.8 - - - +
9E ILE* 1.3 66.0 + - - +
14F TRP* 3.9 20.0 - - + -
24F TYR* 3.1 11.1 - - - +
25F HIS* 2.8 44.6 + - + +
136F GLY 3.3 6.3 - - - +
137F CYS* 2.1 46.9 - - - -
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Residues in contact with ILE 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ILE* 6.1 0.4 - - + -
8E CYS* 1.3 76.0 - - - +
10E GLY* 1.3 65.1 + - - +
10F ILE* 3.6 18.5 - - + +
14F TRP* 3.5 8.2 - - - -
22F TYR* 5.9 0.2 - - + -
23F GLY 3.5 6.5 - - - +
24F TYR* 3.4 38.6 - - + -
115F VAL* 4.2 16.4 - - + +
118F LEU* 4.0 25.8 - - + +
119F TYR* 3.9 37.7 - - + +
122F VAL* 3.7 20.2 - - + -
135F ASN 5.1 0.2 - - - +
136F GLY* 2.9 17.0 + - - +
138F PHE* 4.7 3.4 - - + -
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Residues in contact with GLY 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ILE* 1.3 81.7 - - - +
11E TYR* 1.3 71.7 + - - +
10F ILE* 4.5 6.3 - - - -
12F GLY 5.8 0.2 - - - -
14F TRP* 3.3 25.0 - - - -
17F MET* 4.2 0.2 - - - -
22F TYR* 3.5 5.2 - - - +
23F GLY 3.1 27.9 + - - -
115F VAL* 4.9 2.0 - - - +
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Residues in contact with TYR 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLY* 1.3 81.2 - - - +
12E HIS* 1.3 54.6 + - - +
321E LEU* 3.8 23.8 - - + -
322E ARG 4.3 11.0 - - - -
324E SER* 5.0 3.4 - - - -
6F ILE* 3.9 31.1 - - + +
7F ALA* 3.0 26.2 + - - +
10F ILE* 3.1 35.8 + - + -
12F GLY* 3.3 15.3 + - - -
13F GLY* 3.2 23.2 - - - -
14F TRP* 2.7 36.4 + - - +
17F MET* 3.5 7.4 - - - +
21F TRP 3.2 12.8 - - - +
115F VAL* 4.0 20.6 - - + -
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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