Contacts of the strand formed by residues 100 - 104 (chain E) in PDB entry 3ZPL
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 100 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60E ARG* 3.3 7.1 - - - +
61E MET* 3.2 35.4 + - + +
90E ARG* 3.9 21.5 - - + +
91E GLU 3.4 6.1 + - - +
92E ASP* 3.5 32.1 + - - +
97E LYS 5.6 2.2 + - - -
98E ARG 4.4 2.8 + - - +
99E GLY* 1.3 88.3 + - - +
101E PHE* 1.3 63.7 + - - +
5G A 2.8 39.4 + - - +
6G T 4.3 10.6 + - - +
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Residues in contact with PHE 101 (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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58E ARG* 3.9 23.3 - - + -
59E LEU* 3.7 14.1 - - - -
60E ARG* 3.5 33.2 - - + -
61E MET* 4.4 2.2 - - - -
63E GLU* 5.9 0.9 - - - -
90E ARG* 3.2 13.2 - - - +
91E GLU* 2.7 39.1 + - + +
92E ASP 4.1 14.8 - - - -
93E CYS* 4.1 27.6 - - + -
94E PRO* 4.6 6.3 - - + -
100E GLN* 1.3 74.2 - - - +
102E ALA* 1.3 58.2 - - - +
103E ILE* 4.3 15.5 - - + -
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Residues in contact with ALA 102 (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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51E LEU* 3.6 12.3 - - + +
58E ARG* 3.2 3.5 - - - -
59E LEU 2.9 34.5 + - - +
61E MET* 3.9 17.5 - - + -
64E LEU* 3.9 25.1 - - + -
79E VAL* 4.8 5.2 - - + -
88E VAL* 4.5 10.3 - - + -
89E ARG 3.7 4.3 - - - -
90E ARG* 4.9 1.1 - - - +
100E GLN 4.2 0.2 + - - -
101E PHE* 1.3 71.6 - - - +
103E ILE* 1.3 60.9 + - - +
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Residues in contact with ILE 103 (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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51E LEU* 4.3 2.5 - - - -
56E ARG 4.4 10.1 - - - +
57E ARG* 3.5 9.9 - - + +
58E ARG* 3.7 16.4 - - + -
88E VAL* 3.3 4.6 - - - +
89E ARG* 2.8 85.5 + - + +
91E GLU* 3.7 34.8 - - + +
101E PHE* 4.3 7.9 - - + -
102E ALA* 1.3 77.9 - - - +
104E LEU* 1.3 73.4 + - - +
105E THR 3.5 0.3 + - - -
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Residues in contact with LEU 104 (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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48E LEU* 4.0 25.6 - - + +
51E LEU* 4.0 14.1 - - + +
52E ALA* 3.5 39.7 - - + +
57E ARG* 3.0 33.7 + - + +
87E TRP 3.3 20.2 - - - +
103E ILE* 1.3 79.9 - - - +
105E THR* 1.3 69.2 + - - +
108E GLY* 3.6 22.0 - - - +
109E TYR* 3.9 20.9 - - + +
112E LEU* 4.7 1.6 - - + -
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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