Contacts of the strand formed by residues 91 - 96 (chain D) in PDB entry 1Z6Z
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 ARG 91 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MET 5.6 0.2 + - - -
2D LEU* 3.7 53.5 + - + +
4D ARG 3.2 3.2 + - - +
5D ALA* 3.1 24.5 - - + -
6D VAL 3.0 24.4 + - - -
89D LEU* 3.8 4.7 - - - +
90D GLN* 1.3 80.8 - - - +
92D LEU* 1.3 68.7 + - - +
93D LEU* 4.4 14.9 - - + +
145D LEU* 3.5 5.2 - - - +
146D ASN* 3.3 36.4 + - - +
148D THR* 3.8 19.5 + - - +
242D LEU* 3.9 29.1 + - - +
243D GLU* 4.8 4.6 + - - +
245D ASP* 5.2 3.6 + - - +
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Residues in contact with LEU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D VAL* 3.4 25.8 - - + +
8D LEU* 5.2 2.9 - - + -
89D LEU* 5.7 0.4 - - + -
91D ARG* 1.3 74.1 - - - +
93D LEU* 1.3 64.5 + - - +
94D LEU* 5.3 0.9 - - + +
135D VAL* 3.9 25.4 - - + +
136D LEU* 4.3 8.5 - - + -
139D PHE* 3.6 50.5 - - + +
145D LEU* 3.7 7.5 - - + +
146D ASN 2.9 11.0 + - - +
147D ARG* 4.0 28.7 - - + -
148D THR* 2.9 31.6 + - - +
149D VAL* 6.0 0.9 - - + -
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Residues in contact with LEU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D LEU* 4.0 16.4 - - + -
5D ALA* 5.7 0.9 - - + -
6D VAL 2.9 11.8 + - - +
7D CYS* 3.3 17.5 - - + -
8D LEU* 2.8 33.1 + - - +
24D LEU* 3.8 28.7 - - + -
28D LEU* 5.6 0.7 - - + -
91D ARG* 4.4 14.1 - - + +
92D LEU* 1.3 77.5 - - - +
94D LEU* 1.3 58.5 + - - +
95D ILE* 4.1 16.8 - - + -
148D THR* 3.4 24.9 - - + +
150D VAL* 4.2 3.8 - - + -
242D LEU* 4.0 27.4 - - + -
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Residues in contact with LEU 94 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D LEU* 3.6 24.0 - - + +
10D THR* 5.5 1.8 - - + -
92D LEU* 5.3 0.8 - - + +
93D LEU* 1.3 73.2 - - - +
95D ILE* 1.3 63.6 + - - +
96D ASN* 3.5 19.5 - - - +
131D LEU* 4.0 23.3 - - + +
132D THR* 3.4 48.7 - - + +
135D VAL* 4.5 18.8 - - + -
148D THR 3.0 8.1 + - - -
149D VAL* 4.2 14.6 - - + -
150D VAL* 2.7 35.0 + - - +
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Residues in contact with ILE 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D CYS* 5.0 0.2 - - - -
8D LEU 2.8 16.4 + - - +
9D LEU* 3.8 16.1 - - + +
10D THR* 3.4 20.4 + - - -
20D LEU* 3.8 25.6 - - + -
24D LEU* 3.9 24.5 - - + -
93D LEU* 4.1 23.6 - - + -
94D LEU* 1.3 80.1 - - - +
96D ASN* 1.3 59.8 + - - +
97D ASN* 3.2 8.6 + - + -
150D VAL* 3.7 16.2 - - + -
152D ILE* 4.1 28.9 - - + -
238D LEU* 4.8 6.5 - - + -
239D LEU* 5.8 0.4 - - + -
242D LEU* 4.9 4.5 - - + -
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Residues in contact with ASN 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D THR* 3.9 4.8 + - - -
94D LEU* 3.5 16.7 - - - +
95D ILE* 1.3 67.6 - - - +
97D ASN* 1.3 59.2 + - - +
98D ALA 3.9 0.9 - - - -
128D MET* 3.7 42.1 - - + +
131D LEU* 3.8 18.4 - - - +
132D THR* 3.1 23.1 + - - -
150D VAL 2.8 24.7 + - - +
151D ASN* 4.3 0.7 - - - -
152D ILE* 3.0 25.3 + - - +
174D ARG* 3.2 11.2 + - - +
178D PHE* 3.4 14.3 - - - -
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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