Contacts of the strand formed by residues 153 - 159 (chain A) in PDB entry 3X0Y
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 TYR 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A ALA* 4.2 11.2 - - + -
146A THR 3.2 9.2 - - - +
147A PRO* 3.6 31.2 - - + -
148A THR* 3.7 1.5 + - - -
151A GLY 3.8 15.1 + - - -
152A GLY* 1.3 78.9 - - - -
154A VAL* 1.3 63.5 + - - +
155A LEU* 4.9 1.3 - - + -
177A VAL* 3.9 15.7 - - + -
183A GLN* 2.9 22.6 + - - -
188A ILE* 3.6 43.2 - - + +
223A VAL 4.4 0.2 - - - -
224A LYS* 3.5 8.8 - - - +
225A VAL* 2.8 39.4 + - + -
230A VAL* 4.0 25.5 - - + +
234A PRO* 3.4 15.8 - - - +
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Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ARG* 3.6 1.4 - - - +
145A ALA* 3.2 3.8 - - - -
146A THR* 2.7 47.3 + - + +
148A THR* 3.6 23.6 - - + -
153A TYR* 1.3 79.0 - - - +
155A LEU* 1.3 64.7 + - - +
156A ASN* 4.3 11.2 + - - +
222A ASN* 3.7 35.4 - - + +
223A VAL 3.3 4.3 - - - +
224A LYS* 4.4 10.1 - - + -
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A VAL* 4.8 5.6 - - + -
144A ARG 3.4 4.5 - - - +
145A ALA* 3.5 29.8 - - + -
153A TYR* 4.9 0.7 - - + -
154A VAL* 1.3 74.5 - - - +
156A ASN* 1.3 68.1 + - - +
173A VAL* 3.6 42.0 - - + -
175A GLY* 4.3 11.0 - - - +
188A ILE* 4.2 11.2 - - + -
190A ALA* 5.7 0.2 - - + -
220A PHE* 3.8 21.0 - - + +
222A ASN 3.3 2.8 + - - -
223A VAL* 2.8 40.0 + - + +
225A VAL* 3.7 22.9 - - + -
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Residues in contact with ASN 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LYS 4.2 1.0 - - - +
143A VAL* 3.4 6.5 - - - +
144A ARG* 3.0 78.4 + - + +
146A THR* 5.4 3.4 + - - -
154A VAL* 4.3 11.1 + - - +
155A LEU* 1.3 77.5 + - - +
157A GLY* 1.3 58.0 + - - +
220A PHE* 3.4 4.5 - - - +
221A HIS* 3.7 10.0 - - - -
222A ASN* 3.0 39.2 + - - +
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Residues in contact with GLY 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LYS 5.1 2.2 - - - -
143A VAL* 4.0 11.9 - - - -
144A ARG* 5.8 1.1 - - - -
156A ASN* 1.3 75.4 - - - +
158A THR* 1.3 64.7 + - - -
219A ASP* 3.7 0.5 - - - +
220A PHE* 2.9 36.2 + - - +
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Residues in contact with THR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A GLU* 4.3 9.0 - - - +
134A ASN 5.2 0.2 + - - -
143A VAL* 3.7 14.2 - - - +
157A GLY* 1.3 74.9 + - - -
159A LYS* 1.3 74.4 + - - +
160A HIS* 3.8 27.2 + - + +
217A SER* 4.1 9.0 - - - -
218A THR 3.5 4.3 - - - +
219A ASP* 2.8 29.5 + - - +
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Residues in contact with LYS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ALA* 3.1 42.2 - - + +
131A SER* 3.3 19.1 + - - +
132A SER 3.4 11.2 - - - +
133A GLU* 2.8 28.4 + - + -
141A TRP* 4.6 4.2 - - - -
143A VAL* 3.5 27.0 - - + +
158A THR* 1.3 76.5 - - - +
160A HIS* 1.3 59.3 + - - +
162A CYS* 3.4 19.7 - - - -
173A VAL* 4.6 2.7 - - - -
174A PHE 2.7 26.4 + - - +
175A GLY* 4.9 0.2 - - - -
176A VAL* 5.8 0.2 - - - +
217A SER* 3.2 7.8 - - - -
218A THR 3.0 30.9 + - - +
220A PHE* 4.2 7.5 - - + -
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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