Contacts of the strand formed by residues 134 - 140 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLU 3.9 0.2 - - - -
4A CYS* 3.9 1.6 - - - -
5A ILE* 2.7 34.7 + - - +
132A LEU* 2.3 16.6 + - - +
133A GLN* 1.3 71.5 - - - +
135A PHE* 1.3 64.3 + - - -
164A LYS* 5.0 7.7 - - - +
165A SER 4.1 10.7 + - - -
167A LEU* 5.2 0.7 - - - -
252A LEU* 3.3 17.3 - - - -
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Residues in contact with PHE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 2.7 59.7 - - + -
7A ILE* 4.2 13.7 - - + -
122A ILE* 3.7 26.0 - - + -
126A ALA* 4.8 0.2 - - + -
134A GLY* 1.3 71.7 - - - -
136A SER* 1.3 55.2 + - - +
137A VAL* 5.3 2.0 - - + -
157A LEU* 5.2 8.3 - - + -
161A TYR* 4.1 33.4 - + + -
164A LYS* 4.2 28.9 - - + -
165A SER 3.9 4.4 + - - -
166A LYS* 3.4 20.8 - - + -
167A LEU* 2.4 43.8 + - - +
252A LEU* 4.8 1.0 - - - +
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A CYS* 5.6 5.2 - - - -
5A ILE 2.6 9.7 + - - -
6A SER* 2.7 37.6 - - - -
7A ILE* 2.8 35.5 + - - +
30A ILE* 4.6 4.1 - - - +
134A GLY 4.2 0.2 - - - -
135A PHE* 1.3 75.5 - - - +
137A VAL* 1.3 61.9 - - - +
138A PHE* 4.5 7.6 - - - -
167A LEU* 3.2 8.3 - - - -
169A PHE* 5.0 14.8 - - - -
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 3.3 17.0 - - + -
9A VAL* 3.2 27.8 - - + -
135A PHE* 4.7 3.6 - - + +
136A SER* 1.3 81.5 - - - +
138A PHE* 1.2 60.0 + - - +
139A HIS* 4.2 5.6 - - + -
150A THR* 4.7 1.1 - - + -
153A LEU* 5.6 1.3 - - + -
154A MET* 2.8 46.7 - - + -
157A LEU* 5.1 0.7 - - + -
166A LYS* 5.1 0.2 - - + -
167A LEU 2.9 7.1 + - - +
168A GLU* 3.2 17.9 - - + +
169A PHE* 2.4 38.2 + - - +
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Residues in contact with PHE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A SER* 5.2 3.1 - - - -
7A ILE 3.0 28.0 + - - +
8A HIS* 3.1 29.8 - + - -
9A VAL* 2.5 41.4 - - - +
10A GLY 4.3 0.7 + - - -
13A GLY* 3.3 23.1 - - - -
16A ILE* 2.6 40.6 - - + -
20A CYS* 3.1 41.1 - - + -
21A TRP* 5.0 2.9 - - - -
136A SER* 4.5 12.3 - - - -
137A VAL* 1.2 75.8 - - - +
139A HIS* 1.3 51.4 + - - +
169A PHE* 4.0 22.2 - + - -
235A VAL* 4.7 1.3 - - + -
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Residues in contact with HIS 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 4.5 6.3 - - - -
10A GLY 5.9 0.4 - - - +
12A ALA* 4.6 6.0 - - - +
13A GLY* 5.3 0.2 - - - -
16A ILE* 5.7 0.9 - - - +
137A VAL* 4.2 7.6 - - + -
138A PHE* 1.3 74.8 - - - +
140A SER* 1.3 87.2 + - - +
141A PHE* 3.3 30.2 - + - -
146A GLY 3.9 8.5 - - - -
150A THR* 3.9 19.4 + - + -
168A GLU* 3.4 23.8 - - + -
169A PHE 2.9 18.0 + - - +
170A SER* 3.2 5.1 - - - -
171A ILE* 3.1 24.4 + - - +
189A LEU* 3.7 21.7 + - + -
190A THR* 5.6 0.2 - - - -
193A THR* 3.5 21.2 - - + +
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Residues in contact with SER 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLY* 5.9 2.4 - - - -
12A ALA* 4.0 21.0 - - - +
139A HIS* 1.3 95.1 + - - +
141A PHE* 1.2 67.2 - - - +
142A GLY* 3.3 3.6 - - - -
143A GLY* 3.0 27.9 + - - -
146A GLY* 3.5 17.3 + - - +
171A ILE 3.5 11.9 - - - -
189A LEU* 3.6 2.4 - - - +
500A GTP 4.5 10.5 + - - -
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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