Contacts of the strand formed by residues 153 - 156 (chain C) in PDB entry 3IU3
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 THR 153 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C PRO* 5.6 2.6 - - - +
152C VAL* 1.3 74.2 + - - +
154C VAL* 1.3 72.2 + - - +
155C SER* 4.9 6.3 - - - +
199C ASN 3.2 4.0 - - - +
200C VAL* 3.3 2.8 - - - +
201C ASN* 2.7 60.1 + - + +
203C LYS* 6.2 2.1 - - - +
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Residues in contact with VAL 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C CYS* 5.2 0.4 - - + -
144C VAL* 4.2 17.3 - - + -
152C VAL* 3.9 19.1 - - + -
153C THR* 1.3 84.2 - - - +
155C SER* 1.3 71.7 + - - +
156C TRP* 4.3 6.9 - - - +
165C VAL* 5.9 1.2 - - - +
167C THR* 4.4 18.4 + - + +
180C LEU* 4.4 6.1 - - + -
182C SER* 3.5 34.3 - - - +
198C CYS* 4.3 12.3 - - + -
199C ASN 3.2 7.4 - - - +
200C VAL* 4.4 7.9 - - + -
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Residues in contact with SER 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C THR* 4.9 5.9 - - - +
154C VAL* 1.3 75.3 - - - +
156C TRP* 1.3 64.1 - - - +
158C SER 4.5 0.9 - - - -
159C GLY* 4.0 16.5 + - - -
165C VAL* 6.3 0.2 - - - -
198C CYS* 3.5 2.9 - - - -
199C ASN* 2.6 65.9 + - - +
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Residues in contact with TRP 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C LEU* 3.6 21.1 - - + -
141C GLY* 3.6 37.9 - - - -
142C CYS* 3.8 6.1 - - + -
154C VAL* 4.3 2.3 - - + +
155C SER* 1.3 80.1 - - - +
157C ASN* 1.3 69.4 + - - +
158C SER 3.3 1.6 - - - -
159C GLY* 2.9 10.6 + - - +
160C ALA 3.2 9.7 + - - -
161C LEU* 3.3 33.0 + - + +
165C VAL* 3.6 31.5 - - + +
182C SER* 3.1 26.7 + - - -
183C VAL 4.6 1.4 + - - +
184C VAL* 4.2 15.3 - - + -
196C TYR* 4.4 7.4 - + + -
197C ILE 3.4 25.1 - - - -
198C CYS* 3.6 27.1 - - + -
213C VAL* 3.8 12.6 - - + -
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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
------------------------------------------------------------
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