Contacts of the strand formed by residues 155 - 161 (chain D) in PDB entry 2ZSU
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 PHE 155 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ARG* 3.5 44.9 - - + +
80D VAL 4.1 2.0 - - - -
81D LEU* 3.6 42.2 - - + -
104D ILE* 3.9 13.2 - - + -
148D PHE* 3.8 23.1 - + - -
149D ILE* 4.7 0.2 - - + -
152D ASN* 4.0 11.2 - - + -
153D SER* 3.8 27.6 - - - -
154D GLY* 1.3 76.7 - - - +
156D ASP* 1.3 64.5 + - - +
157D VAL 3.9 14.4 - - - +
158D ILE* 3.9 9.4 - - + -
184D ALA* 3.1 14.9 + - + +
185D LEU* 3.3 8.8 - - - +
186D ASN* 2.9 21.6 + - - -
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Residues in contact with ASP 156 (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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74D HIS* 3.3 29.5 - - + +
76D ASN 3.6 10.0 - - - +
77D PRO* 4.0 11.0 - - + -
78D ARG* 2.9 18.6 + - - +
79D ARG* 2.8 34.2 + - - +
154D GLY 4.3 0.2 + - - -
155D PHE* 1.3 73.4 - - - +
157D VAL* 1.3 56.0 + - - +
185D LEU* 4.5 0.2 - - - -
186D ASN* 3.0 25.1 + - - +
188D PRO 4.1 1.7 - - - +
189D GLY* 3.1 7.5 - - - -
190D ILE 2.7 30.2 + - - -
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Residues in contact with VAL 157 (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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70D ALA* 4.6 9.6 - - + +
71D MET* 4.0 10.5 - - - -
74D HIS* 4.2 6.5 - - + -
77D PRO* 3.7 28.7 - - + -
79D ARG 3.5 2.8 + - - -
80D VAL* 3.4 12.1 - - + +
81D LEU 2.8 25.5 + - - -
155D PHE* 3.9 2.1 - - - +
156D ASP* 1.3 86.1 - - - +
158D ILE* 1.3 69.7 + - - +
159D ILE* 3.8 30.1 - - + -
190D ILE* 3.1 26.7 - - + +
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Residues in contact with ILE 158 (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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81D LEU* 3.5 24.5 - - + -
83D ILE* 5.1 4.5 - - + -
149D ILE* 4.3 10.3 - - + -
155D PHE* 3.9 13.2 - - + -
157D VAL* 1.3 78.5 - - - +
159D ILE* 1.3 64.6 + - - +
160D VAL* 4.4 9.2 - - + -
177D PHE* 5.7 0.4 - - + -
181D ALA* 3.6 30.5 - - + +
184D ALA* 4.0 15.5 - - + -
185D LEU* 3.7 16.8 - - + +
190D ILE 2.8 8.3 + - - +
191D TYR* 3.3 26.3 - - + -
192D VAL* 2.9 29.5 + - - +
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Residues in contact with ILE 159 (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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66D LEU* 4.0 34.8 - - + +
67D VAL* 4.1 19.1 - - + +
71D MET* 4.7 2.7 - - - -
80D VAL* 4.2 7.9 - - + -
81D LEU 2.8 12.5 + - - +
82D ILE* 3.3 10.7 - - + +
83D ILE 2.9 24.8 + - - -
90D ALA* 4.8 2.7 - - + -
94D VAL* 3.6 31.4 - - + -
157D VAL* 3.8 18.6 - - + -
158D ILE* 1.3 76.3 - - - +
160D VAL* 1.3 65.5 + - - +
161D ASP* 3.7 5.3 + - + +
192D VAL* 3.5 18.4 - - + -
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Residues in contact with VAL 160 (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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66D LEU* 4.2 3.3 - - - +
83D ILE* 3.8 17.3 - - + +
158D ILE* 4.4 2.7 - - + -
159D ILE* 1.3 75.3 - - - +
161D ASP* 1.3 58.1 + - - +
162D SER* 3.8 21.9 + - - +
172D LEU* 4.1 21.1 - - + +
173D PHE* 5.5 1.1 - - + -
177D PHE* 4.2 12.6 - - + -
191D TYR* 3.4 36.3 - - + +
192D VAL 2.9 9.9 + - - -
193D THR* 3.7 19.7 + - - +
194D GLN* 3.6 23.1 + - - +
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Residues in contact with ASP 161 (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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62D TYR* 2.7 36.2 + - - -
63D HIS* 4.2 10.6 + - - -
66D LEU* 3.7 19.5 - - + -
82D ILE* 4.9 1.8 - - + -
83D ILE 2.9 13.3 + - - +
84D GLY* 3.6 0.3 - - - -
85D GLY* 3.0 40.4 + - - +
87D ASP* 4.2 5.4 - - - +
90D ALA* 4.0 15.8 + - + +
159D ILE* 3.7 4.4 + - + -
160D VAL* 1.3 71.6 - - - +
162D SER* 1.3 59.5 + - - +
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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