Contacts of the strand formed by residues 153 - 159 (chain B) in PDB entry 1ZDR
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 HIS 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B LEU* 4.2 22.1 - - + +
26B ALA* 4.2 9.1 - - + +
27B ASP 5.8 0.2 - - - -
115B THR* 4.6 3.6 - - + -
116B LYS 3.0 15.9 - - - +
117B ILE* 4.2 6.7 - - + -
118B PHE* 3.8 8.4 - - - -
142B PRO* 3.7 2.9 - - - +
143B GLY* 2.7 44.4 + - - +
144B GLY 3.4 34.5 + - - -
149B ASN* 4.1 13.9 - - + -
151B TYR 2.8 23.8 + - - +
152B GLU* 1.3 77.1 + - - +
154B ALA* 1.3 59.1 + - - +
155B PHE* 3.8 28.4 - + - -
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Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B VAL 3.5 1.2 - - - +
115B THR* 3.3 5.4 - - - +
116B LYS* 2.9 31.4 + - + +
118B PHE* 3.9 8.5 - - + -
140B TYR* 3.3 42.6 - - + +
141B THR 3.4 10.8 - - - +
142B PRO* 4.2 1.3 - - + -
143B GLY 4.0 1.3 - - - +
153B HIS* 1.3 78.3 - - - +
155B PHE* 1.3 64.5 + - - +
156B ILE* 3.7 5.9 + - + +
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Residues in contact with PHE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ALA* 3.9 23.3 - - + -
27B ASP* 3.7 10.1 - - - -
30B TYR* 3.5 52.0 - + + +
114B VAL 3.8 2.5 - - - -
115B THR* 3.3 31.2 - - + -
139B SER* 4.0 1.9 + - - +
140B TYR* 3.6 2.4 - - - -
141B THR* 2.8 58.0 + - + +
143B GLY* 4.1 9.0 - - - -
153B HIS* 3.8 27.4 - + - -
154B ALA* 1.3 71.2 - - - +
156B ILE* 1.3 60.7 + - - +
157B ILE* 5.5 1.1 - - - +
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Residues in contact with ILE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B TYR* 5.2 1.2 + - - -
112B LEU 3.6 0.2 - - - +
113B TYR* 3.5 2.6 - - - -
114B VAL* 2.7 47.3 + - + +
116B LYS* 3.7 45.8 - - + +
118B PHE* 5.8 0.4 - - + -
137B ILE* 4.0 18.2 - - + -
139B SER 3.5 10.8 - - - +
140B TYR* 3.8 30.1 - - + -
154B ALA* 4.1 7.2 - - + +
155B PHE* 1.3 77.7 - - - +
157B ILE* 1.3 66.6 + - - +
158B TYR* 3.3 30.7 - - + +
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Residues in contact with ILE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B TYR* 4.4 10.3 - - - +
111B ARG* 3.9 29.6 - - + +
112B LEU 3.3 3.4 - - - +
113B TYR* 3.8 31.2 - - + -
137B ILE* 3.5 5.4 - - - +
138B VAL* 3.0 39.4 + - + -
139B SER* 3.0 34.1 + - - +
155B PHE 5.5 1.3 - - - +
156B ILE* 1.3 79.4 - - - +
158B TYR* 1.3 64.7 + - - +
159B GLU* 4.8 0.2 - - - +
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Residues in contact with TYR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ARG* 3.4 3.8 - - - +
112B LEU* 2.9 47.4 + - + +
114B VAL* 3.8 32.5 - - + -
116B LYS* 3.0 29.6 + - - -
130B ILE* 4.1 30.1 - - + +
135B TRP* 3.9 12.1 - - + -
136B GLU 3.0 17.7 - - - -
137B ILE* 3.4 24.2 - - + +
138B VAL* 4.7 0.2 - - - -
156B ILE* 3.3 30.3 - - + +
157B ILE* 1.3 74.6 - - - +
159B GLU* 1.3 69.1 + - - +
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Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ASP 3.6 12.6 - - - +
111B ARG* 2.8 41.6 + - + +
135B TRP* 3.2 8.2 - - - -
136B GLU* 2.7 34.9 + - - +
138B VAL* 3.5 36.0 - - + +
157B ILE* 4.8 0.2 - - - +
158B TYR* 1.3 80.1 - - - +
160B ARG* 1.3 65.7 + - - +
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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