Contacts of the strand formed by residues 134 - 140 (chain B) in PDB entry 1TUB
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 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B GLU 3.4 8.3 + - - -
4B ILE* 4.3 1.1 - - - -
5B VAL* 3.1 32.5 + - - +
132B LEU* 4.8 0.9 - - - +
133B GLN* 1.2 81.8 + - - +
135B PHE* 1.3 66.7 - - - -
136B GLN* 3.9 9.0 - - - -
165B ILE 4.6 1.1 - - - -
167B ASN* 3.8 14.4 - - - -
252B LEU* 3.8 7.7 - - - +
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Residues in contact with PHE 135 (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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5B VAL* 3.3 33.0 - - + -
7B ILE* 3.7 4.3 - - + -
122B VAL* 3.7 23.1 - - + -
126B SER* 6.0 0.7 - - - -
134B GLY* 1.3 73.7 - - - -
136B GLN* 1.3 56.4 + - - +
157B ILE* 3.1 35.2 - - + -
161B TYR* 4.1 26.0 - + + -
164B ARG* 4.4 20.2 - - + -
165B ILE 4.3 2.6 + - - -
166B MET* 2.2 59.9 - - + +
167B ASN* 2.4 39.2 + - - +
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Residues in contact with GLN 136 (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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4B ILE* 3.3 14.1 - - + +
5B VAL 2.8 12.9 + - - +
6B HIS* 2.9 25.4 + - - +
7B ILE 2.7 37.5 + - - +
20B PHE* 4.4 7.0 - - - -
30B ILE* 2.9 13.3 - - - +
134B GLY* 4.5 1.3 - - - -
135B PHE* 1.3 82.1 - - - +
137B LEU* 1.3 59.2 + - - +
138B THR* 5.9 0.4 - - - -
167B ASN* 3.4 13.7 - - + +
169B PHE* 4.4 13.2 - - + -
239B THR* 3.7 10.4 - - + +
243B ARG* 2.9 41.2 - - - +
252B LEU* 4.9 0.8 - - - +
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Residues in contact with LEU 137 (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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7B ILE* 2.3 64.6 - - + -
9B ALA* 6.5 0.2 - - + -
136B GLN* 1.3 77.3 - - - +
138B THR* 1.3 65.7 - - - +
139B HIS* 4.5 3.1 - - + +
150B GLY* 4.8 2.2 - - - +
153B LEU* 5.1 2.5 - - + -
154B ILE* 3.8 31.4 - - + +
157B ILE* 4.4 6.7 - - + -
166B MET* 3.8 23.3 - - + -
167B ASN 3.5 4.2 + - - -
168B THR* 3.7 16.1 - - + -
169B PHE* 3.0 33.1 + - - +
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Residues in contact with THR 138 (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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7B ILE 3.3 4.6 + - - +
8B GLN* 3.5 10.7 - - + +
9B ALA* 3.3 26.7 + - - +
12B CYS 4.3 2.0 - - - -
13B GLY* 2.2 49.9 + - - +
16B ILE* 4.1 20.9 - - + -
17B GLY* 4.9 1.1 - - - +
20B PHE* 6.1 1.1 - - + -
136B GLN 5.9 0.2 - - - -
137B LEU* 1.3 74.6 - - - +
139B HIS* 1.3 67.4 + - - +
169B PHE* 4.1 20.0 - - + -
235B MET* 5.4 2.7 - - + -
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Residues in contact with HIS 139 (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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9B ALA 4.6 4.9 - - - -
12B CYS* 4.5 3.3 - - - -
13B GLY* 4.1 2.0 - - - -
137B LEU* 4.5 5.8 - - + +
138B THR* 1.3 82.2 - - - +
140B SER* 1.5 71.9 + - - +
141B LEU* 4.0 14.6 - - + -
146B GLY* 3.7 24.9 - - - +
147B SER* 4.6 2.5 - - - -
150B GLY* 4.7 12.3 - - - -
154B ILE* 5.2 5.4 - - + -
168B THR* 5.8 3.8 - - - -
169B PHE* 3.5 17.0 + - - +
170B SER* 3.5 15.2 - - - -
171B VAL* 3.1 27.5 + - - +
189B LEU* 4.5 2.8 - - - +
192B HIS* 5.1 3.4 - + - -
193B GLN* 2.5 40.0 + - - -
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Residues in contact with SER 140 (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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9B ALA 6.1 0.4 - - - -
10B GLY* 5.4 0.5 - - - -
11B GLN 5.2 0.9 + - - -
12B CYS* 3.8 14.8 - - - -
13B GLY 5.6 0.2 - - - -
139B HIS* 1.5 65.4 - - - +
141B LEU* 1.3 54.3 + - - +
143B GLY* 2.6 12.6 + - - -
146B GLY* 4.0 9.2 - - - -
147B SER* 2.3 31.6 + - - -
171B VAL* 3.9 5.4 - - - -
189B LEU* 4.1 4.0 - - - -
500B GDP 2.7 50.2 + - - -
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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