Contacts of the strand formed by residues 135 - 140 (chain Q) in PDB entry 3QUM
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 135 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133Q GLY 4.2 0.2 + - - -
134Q THR* 1.3 78.5 - - - +
136Q CYS* 1.3 59.6 + - - +
160Q LEU 3.7 6.7 - - - +
161Q HIS* 4.2 0.2 - - - -
185Q ARG* 4.2 21.5 - - - +
201Q CYS* 3.4 23.9 - - - +
202Q ASN* 3.7 21.2 + - - -
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Residues in contact with CYS 136 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97K TYR* 4.8 3.6 + - - -
134Q THR 4.6 5.4 - - - +
135Q THR* 1.3 76.5 - - - +
137Q TYR* 1.3 66.5 + - - +
159Q ASP* 4.0 3.6 - - - +
160Q LEU* 2.9 36.9 + - + +
161Q HIS* 4.6 2.0 - - - +
162Q VAL* 4.6 9.9 - - - -
183Q ALA* 6.0 0.9 - - + -
199Q LEU* 4.0 22.4 - - + -
200Q VAL 3.2 6.5 - - - -
201Q CYS* 2.0 51.6 - - - +
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Residues in contact with TYR 137 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97K TYR* 3.6 54.6 - + + +
27Q GLN* 3.2 39.0 + - - -
29Q TRP* 4.0 8.3 - - - -
136Q CYS* 1.3 78.1 - - - +
138Q ALA* 1.3 72.3 + - - +
139Q SER* 4.5 4.5 - - - -
157Q CYS* 4.1 6.7 - - + -
158Q VAL 3.5 14.8 - - - +
160Q LEU* 4.6 2.7 - - - +
198Q PRO 4.0 0.2 - - - +
199Q LEU* 3.2 20.7 - - - +
200Q VAL* 3.1 60.5 + - + +
201Q CYS* 6.0 0.2 - - - -
202Q ASN 6.3 0.4 - - - -
203Q GLY* 6.0 0.7 - - - -
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Residues in contact with ALA 138 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137Q TYR* 1.3 79.6 - - - +
139Q SER* 1.3 60.9 + - - +
156Q GLN 3.6 0.2 - - - +
157Q CYS* 2.9 27.4 - - - +
158Q VAL* 3.2 21.5 + - + +
160Q LEU* 4.4 11.7 - - + -
192Q SER* 4.9 6.3 - - - +
197Q GLY* 6.0 1.3 - - - -
198Q PRO 3.7 11.7 - - - +
199Q LEU* 4.6 0.9 - - + -
219Q PRO* 6.5 0.9 - - + -
228Q TYR* 4.1 18.6 - - - +
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Residues in contact with SER 139 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22Q CYS* 4.5 0.7 - - - -
27Q GLN* 4.5 7.1 + - - -
30Q GLN* 2.7 43.5 + - - +
137Q TYR* 4.5 5.4 - - - -
138Q ALA* 1.3 76.9 - - - +
140Q GLY* 1.3 59.2 + - - +
155Q LEU* 3.8 4.5 - - - -
156Q GLN 3.0 4.7 - - - -
157Q CYS* 3.5 20.9 - - - -
192Q SER 4.7 3.9 - - - +
194Q ASP 5.1 0.7 - - - +
197Q GLY* 4.0 16.5 - - - -
198Q PRO* 3.9 15.0 + - - +
200Q VAL* 5.9 1.0 - - - +
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Residues in contact with GLY 140 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Q GLN* 5.1 0.7 - - - -
139Q SER* 1.3 74.7 - - - +
141Q TRP* 1.3 59.8 + - - -
155Q LEU* 3.1 13.5 - - - +
156Q GLN* 2.7 42.8 + - - +
192Q SER 4.1 3.0 + - - -
193Q GLY* 3.1 25.3 - - - -
194Q ASP 4.2 1.6 - - - -
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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