Contacts of the strand formed by residues 168 - 175 (chain B) in PDB entry 3RAW
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 GLY 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B HIS* 3.5 23.6 - - - -
164B GLU* 3.6 0.3 - - - -
165B GLY 2.9 27.6 + - - +
166B THR 3.4 3.8 + - - -
167B PHE* 1.3 87.0 - - - +
169B LYS* 1.3 62.4 + - - +
187B ILE 3.3 11.2 - - - -
189B ARG* 4.0 4.6 - - - +
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Residues in contact with LYS 169 (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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143B HIS* 4.8 13.5 - - + +
144B LEU* 3.7 21.3 - - + +
146B CYS* 3.9 28.9 + - - -
161B ASN* 3.7 25.3 + - - +
163B GLY 3.6 10.8 - - - +
164B GLU* 4.0 15.9 - - + +
167B PHE* 3.7 3.3 - - - -
168B GLY* 1.3 75.4 - - - +
170B VAL* 1.3 63.2 + - - +
171B VAL* 4.3 11.0 - - + -
186B LYS* 3.5 2.6 - - - -
187B ILE* 2.8 47.5 + - + +
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Residues in contact with VAL 170 (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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2B 3RA 3.7 46.9 - - + +
161B ASN* 3.7 1.6 + - - -
162B LEU* 2.9 46.9 + - + -
163B GLY 2.8 17.3 + - - +
167B PHE* 3.8 13.7 - - + -
169B LYS* 1.3 79.7 - - - +
171B VAL* 1.3 67.8 + - - +
184B ALA* 4.0 15.3 - - + -
185B LEU 3.4 11.4 - - - +
186B LYS* 4.2 11.0 - - + +
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Residues in contact with VAL 171 (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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146B CYS* 4.9 4.3 - - - -
158B ILE* 4.0 20.4 - - + -
160B GLY 3.3 13.9 - - - +
161B ASN* 4.0 19.7 - - - +
162B LEU* 3.9 6.3 - - - +
169B LYS* 4.3 18.6 - - + -
170B VAL* 1.3 79.4 - - - +
172B GLU* 1.3 58.7 + - - +
173B CYS* 4.0 18.2 - - - -
184B ALA* 3.6 1.6 - - - -
185B LEU* 2.8 40.3 + - + +
187B ILE* 4.0 20.2 - - + -
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Residues in contact with GLU 172 (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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158B ILE* 3.5 4.9 - - - -
159B VAL* 2.9 46.4 + - + +
160B GLY* 2.8 19.4 + - - +
162B LEU* 3.7 24.7 - - + +
171B VAL* 1.3 74.0 - - - +
173B CYS* 1.3 63.8 + - - +
174B LEU* 4.4 2.3 - - - +
182B GLN* 3.2 26.9 + - + +
183B VAL 3.5 12.6 - - - +
238B LEU* 3.9 23.8 - - + +
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Residues in contact with CYS 173 (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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156B TYR* 4.2 9.2 - - + -
157B GLU 3.2 10.3 - - - +
158B ILE* 3.9 20.9 - - - -
159B VAL* 4.3 0.7 - - - -
171B VAL* 4.0 7.9 - - - -
172B GLU* 1.3 81.1 - - - +
174B LEU* 1.3 71.8 + - - +
182B GLN* 3.5 5.2 - - - -
183B VAL* 3.0 44.0 + - + +
185B LEU* 3.8 35.7 - - - -
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Residues in contact with LEU 174 (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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155B ARG 3.0 17.0 - - - +
156B TYR* 3.4 2.6 - - - -
157B GLU* 3.0 32.7 + - - +
159B VAL* 3.6 30.7 - - + -
172B GLU* 4.4 1.6 - - - +
173B CYS* 1.3 81.5 - - - +
175B ASP* 1.3 59.6 + - - +
176B HIS* 3.4 21.5 + - + +
180B LYS* 3.9 22.2 - - + +
181B SER 3.8 3.1 - - - -
182B GLN* 4.3 14.8 - - + -
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Residues in contact with ASP 175 (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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155B ARG* 2.8 44.9 + - - +
156B TYR* 3.8 18.4 + - + -
173B CYS 4.2 0.2 - - - -
174B LEU* 1.3 68.3 - - - +
176B HIS* 1.3 57.5 + - - +
177B ALA 3.2 6.9 + - - -
178B ARG* 2.9 33.9 + - - +
179B GLY 3.4 0.9 + - - -
180B LYS* 3.1 14.4 + - - -
181B SER* 2.8 25.1 + - - +
183B VAL* 4.1 14.3 - - + +
223B SER* 5.7 2.6 + - - -
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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