Contacts of the strand formed by residues 153 - 161 (chain B) in PDB entry 3R9X
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B THR* 4.6 5.2 + - + +
115B VAL* 4.3 23.6 - - + -
118B LYS* 3.2 36.3 - - + +
121B VAL* 2.4 39.8 + - + +
122B PRO 4.4 2.2 - - - -
123B LEU* 4.5 1.3 - - - -
124B ALA* 5.5 1.3 - - + -
149B VAL* 2.8 23.5 + - + +
150B ARG* 3.3 23.2 + - - +
151B THR 3.8 0.2 - - - -
152B PHE* 1.3 88.5 - - + +
154B ASP* 1.3 67.2 + - - +
155B VAL* 3.8 1.9 + - - +
179B LEU* 3.9 22.9 - - + -
180B VAL 3.5 24.7 - - - +
181B LYS* 3.5 18.4 - - + -
184B LYS* 3.5 8.7 + - - -
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Residues in contact with ASP 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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150B ARG* 5.6 0.4 - - - -
153B TYR* 1.3 72.7 - - - +
155B VAL* 1.3 60.2 + - - +
156B ASN* 3.7 14.8 + - - +
178B LYS 3.5 4.5 - - - +
179B LEU* 3.6 2.8 - - - -
180B VAL* 2.9 36.1 + - + +
182B ASN* 3.1 26.8 + - - +
184B LYS* 2.7 29.0 + - - +
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 4.3 13.0 - - + +
137B GLN* 4.0 40.9 - - + +
149B VAL* 3.9 23.8 - - + -
150B ARG* 3.8 30.0 - - + +
153B TYR 3.8 0.4 + - - -
154B ASP* 1.3 74.9 - - - +
156B ASN* 1.3 61.0 + - - +
157B TYR 3.8 1.4 + - - -
177B ILE* 4.7 15.0 - - + -
178B LYS 3.9 2.0 - - - -
179B LEU* 4.2 14.8 - - + -
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Residues in contact with ASN 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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154B ASP* 4.1 13.5 + - - +
155B VAL* 1.3 75.1 - - - +
157B TYR* 1.3 64.4 + - - +
158B VAL* 3.4 2.2 + - + -
177B ILE* 3.4 4.2 - - - -
178B LYS* 2.8 58.2 + - + +
180B VAL* 3.3 32.3 - - - +
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Residues in contact with TYR 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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130B LYS* 3.2 18.9 + - + +
133B ALA* 4.5 9.6 - - + -
134B GLU* 5.3 2.7 - - + -
137B GLN* 3.7 28.4 + - - +
155B VAL 3.8 3.4 + - - -
156B ASN* 1.3 70.1 - - - +
158B VAL* 1.3 64.6 + - - +
159B MET* 3.6 18.8 - - - -
160B THR* 3.0 27.2 + - - +
175B ALA* 3.5 27.4 - - + +
176B VAL 4.1 1.8 - - - -
177B ILE* 4.5 13.9 - - + -
502B ACT 3.4 44.2 - - + +
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Residues in contact with VAL 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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21B LYS* 3.8 31.8 - - + -
25B GLU* 3.9 26.9 - - + +
125B VAL* 6.1 0.2 - - + -
156B ASN* 4.0 1.6 - - + +
157B TYR* 1.3 77.2 - - - +
159B MET* 1.3 70.3 + - + +
176B VAL* 2.9 30.2 + - + +
178B LYS* 3.7 32.3 - - + +
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Residues in contact with MET 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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18B VAL* 5.1 11.7 - - + +
21B LYS* 4.0 32.3 - - - -
157B TYR* 3.6 11.4 - - - -
158B VAL* 1.3 84.5 - - + +
160B THR* 1.3 76.4 + - - +
161B VAL* 4.4 8.1 - - + -
162B PRO* 5.5 0.4 - - + -
165B PHE* 4.8 20.4 - - + -
175B ALA* 3.3 5.5 - - - +
176B VAL* 2.9 52.2 + - + -
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Residues in contact with THR 160 (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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130B LYS* 3.9 7.2 + - + +
157B TYR* 3.0 26.3 + - - +
159B MET* 1.3 91.5 - - - +
161B VAL* 1.3 64.1 + - - +
162B PRO* 3.4 12.2 - - + +
173B GLN* 3.7 28.9 - - - +
174B SER 3.8 7.4 - - - +
501B ACT 2.9 40.6 + - - +
502B ACT 4.2 0.2 - - - +
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Residues in contact with VAL 161 (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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18B VAL* 5.2 7.9 - - + -
127B MET* 3.9 13.9 - - + -
159B MET* 4.2 8.7 - - + +
160B THR* 1.3 77.1 - - - +
162B PRO* 1.3 68.4 - - + +
165B PHE* 4.1 17.3 - - + -
166B PHE* 3.5 29.1 - - + -
173B GLN* 3.8 2.7 - - - -
174B SER* 2.7 40.9 + - - +
175B ALA* 3.8 16.2 - - - -
176B VAL* 3.9 22.2 - - + -
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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