Contacts of the strand formed by residues 170 - 175 (chain B) in PDB entry 4X61
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 VAL 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B SER* 2.8 27.7 + - - -
130B THR* 4.1 1.7 - - - +
143B GLY* 4.2 2.9 - - - -
144B SER 3.2 22.8 + - - +
147B ILE* 3.4 25.8 - - - +
148B CYS 3.7 9.9 - - - +
149B ILE* 4.0 11.9 - - + -
166B HIS* 3.9 19.1 - - + -
168B ALA 4.4 1.3 - - - +
169B GLN* 1.3 72.4 + - - +
171B THR* 1.3 59.7 + - - +
172B CYS 4.2 4.0 - - - +
173B VAL* 3.9 28.3 - - + -
185B SER* 4.6 1.1 - - - -
186B CYS 3.7 10.3 - - - +
187B SER* 3.9 4.0 - - - -
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Residues in contact with THR 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B SER* 4.3 8.2 + - - +
130B THR* 3.5 13.9 - - - +
169B GLN* 3.8 10.4 + - - +
170B VAL* 1.3 73.5 - - - +
172B CYS* 1.3 60.2 + - - +
186B CYS* 3.0 11.5 + - - -
187B SER* 3.8 14.4 - - - -
188B GLU* 3.8 16.2 + - - +
215B PRO 4.0 8.5 + - - -
216B THR* 3.3 36.3 - - + +
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Residues in contact with CYS 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B THR* 3.6 7.2 - - - +
170B VAL 3.6 0.8 - - - -
171B THR* 1.3 80.8 - - - +
173B VAL* 1.3 74.9 + - - +
174B ALA* 4.9 0.7 - - - -
185B SER* 3.3 4.9 - - - -
186B CYS* 3.1 36.2 + - - +
216B THR 3.8 17.0 - - - +
217B SER* 4.3 2.0 - - - -
218B LEU* 3.5 42.3 - - - +
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B THR* 3.1 34.3 + - + +
131B VAL* 4.2 3.4 - - - +
132B SER* 3.4 11.5 + - - -
141B VAL* 3.6 36.6 - - + +
143B GLY* 3.9 8.3 - - - +
149B ILE* 4.0 14.8 - - + -
170B VAL* 3.9 15.5 - - + -
172B CYS* 1.3 82.7 - - - +
174B ALA* 1.3 61.7 + - - +
183B PHE* 5.1 0.7 - - + -
184B LEU 3.3 6.7 - - - +
185B SER* 3.8 18.4 - - - -
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Residues in contact with ALA 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B SER* 3.6 4.3 - - - +
141B VAL* 5.2 0.2 - - - -
172B CYS* 4.9 1.3 - - - -
173B VAL* 1.3 73.4 - - - +
175B ALA* 1.3 60.1 + - - +
183B PHE* 3.8 3.1 - - - -
184B LEU* 2.8 39.6 + - + -
218B LEU* 4.1 33.2 - - + +
219B ALA* 5.2 1.1 - - - -
220B TRP* 2.9 25.2 + - + +
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Residues in contact with ALA 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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132B SER* 3.0 20.5 + - - +
133B VAL 3.3 28.5 - - - +
134B LEU* 3.7 26.5 - - + -
141B VAL* 4.7 1.7 - - + +
174B ALA* 1.3 72.0 - - - +
176B SER* 1.3 67.3 + - - +
177B PRO* 3.7 1.2 - - - +
183B PHE* 3.5 10.5 - - - +
220B TRP* 3.1 11.7 - - - -
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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
------------------------------------------------------------
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