Contacts of the strand formed by residues 130 - 138 (chain A) in PDB entry 1UWV
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 ARG 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A ARG* 3.1 39.5 + - - +
129A ARG* 1.3 83.9 - - + +
131A ALA* 1.3 63.6 + - - +
165A LEU* 4.3 3.1 - - - -
169A LEU* 4.2 1.3 - - - -
193A GLU* 6.5 0.2 - - + -
194A LEU 3.2 12.6 - - - +
195A VAL* 4.1 16.2 - - + -
263A PHE* 3.2 31.0 - - - -
264A ILE* 2.9 43.8 + - - +
266A VAL* 3.5 32.6 - - + +
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Residues in contact with ALA 131 (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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128A ARG* 4.4 8.3 - - - +
130A ARG* 1.3 77.6 - - - +
132A ARG* 1.3 59.4 + - - +
133A LEU* 3.9 6.1 + - + +
148A PHE* 4.2 22.7 - - + -
165A LEU* 3.5 26.8 - - + +
192A VAL 4.0 0.9 - - - +
193A GLU* 3.4 5.6 - - - +
194A LEU* 3.0 36.7 + - + +
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Residues in contact with ARG 132 (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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128A ARG* 5.4 1.2 - - - +
131A ALA* 1.3 72.0 - - - +
133A LEU* 1.3 62.6 + - - +
134A SER* 3.9 5.5 + - - +
148A PHE* 3.4 19.1 - - - -
191A HIS* 2.7 53.2 + - + +
192A VAL 3.7 3.4 - - - +
193A GLU* 3.5 17.0 + - + -
1434A NI 3.0 12.5 - - - +
1435A PO4 3.5 14.5 + - - -
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Residues in contact with LEU 133 (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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131A ALA* 5.0 6.5 - - + +
132A ARG* 1.3 73.2 - - - +
134A SER* 1.3 62.6 + - - +
135A LEU* 4.1 0.2 - - - +
146A MSE 4.0 20.6 - - + -
147A GLY* 3.5 22.2 - - - +
148A PHE* 3.7 26.5 - - + -
159A VAL* 4.4 6.1 - - + -
165A LEU* 6.0 0.7 - - + -
173A LEU* 3.8 30.1 - - + -
176A VAL* 5.6 1.1 - - + -
191A HIS* 3.4 5.0 - - - -
192A VAL* 2.9 57.2 + - + +
194A LEU* 4.1 20.2 - - + -
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Residues in contact with SER 134 (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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132A ARG* 3.9 5.9 + - - +
133A LEU* 1.3 74.1 - - - +
135A LEU* 1.3 60.2 + - - +
145A GLN 3.7 0.2 - - - +
146A MSE 3.3 6.1 - - - -
147A GLY 2.8 34.3 + - - -
148A PHE* 5.0 2.0 - - - -
149A ARG* 4.8 12.7 - - - +
156A ILE* 3.7 24.4 - - - +
190A GLY 4.4 0.9 - - - -
191A HIS* 4.2 9.1 - - - +
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A LEU 4.1 4.3 - - - +
134A SER* 1.3 76.9 - - - +
136A ASN* 1.3 62.9 + - - +
144A LEU* 4.4 16.8 - - + -
145A GLN 3.2 4.9 - - - +
146A MSE 3.5 36.6 - - + -
156A ILE* 4.1 1.1 - - - +
180A LEU* 3.9 30.1 - - + -
189A LEU* 3.8 35.3 - - + +
190A GLY* 3.3 18.9 + - - +
191A HIS* 3.8 24.5 - - - +
192A VAL* 4.1 2.9 - - + +
205A LEU* 4.0 5.4 - - + -
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Residues in contact with ASN 136 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LEU* 1.3 77.0 + - - +
137A TYR* 1.3 74.1 + - - +
138A LEU* 3.8 11.8 - - - +
143A GLN 3.9 0.2 - - - +
144A LEU* 3.7 5.8 - - - +
145A GLN* 2.8 55.7 + - + +
156A ILE* 3.4 22.2 - - + +
189A LEU 5.6 0.7 - - - -
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Residues in contact with TYR 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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136A ASN* 1.3 86.8 + - - +
138A LEU* 1.3 65.0 + - - +
139A PRO* 3.4 42.6 + - + +
142A GLN* 3.8 31.2 - - + +
143A GLN 3.7 2.9 - - - -
144A LEU* 4.8 1.8 - - - -
186A MSE 3.2 40.6 - - + +
187A ARG* 3.5 67.0 + - + +
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Residues in contact with LEU 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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136A ASN* 3.8 20.2 - - - +
137A TYR* 1.3 76.4 - - - +
139A PRO* 1.3 59.8 - - + +
140A LYS* 3.4 2.2 - - + +
141A THR* 3.4 19.9 + - - +
142A GLN* 2.7 36.9 + - - -
143A GLN* 2.9 31.2 + - + +
145A GLN* 3.8 33.0 - - + +
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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