Contacts of the strand formed by residues 143 - 149 (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 GLN 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A ASN 3.9 0.5 - - - +
137A TYR* 3.7 3.6 - - - -
138A LEU* 2.9 46.5 + - + +
141A THR* 2.8 39.1 + - - +
142A GLN* 1.3 78.0 - - - +
144A LEU* 1.3 63.3 + - - +
186A MSE 4.0 4.7 - - - -
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Residues in contact with LEU 144 (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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135A LEU* 4.4 17.9 - - + -
136A ASN 3.7 20.0 - - - +
137A TYR* 4.7 1.6 - - - +
143A GLN* 1.3 74.6 - - - +
145A GLN* 1.3 71.8 + - - +
146A MSE 5.2 3.4 - - + -
158A ASP* 3.9 1.9 - - - +
177A ARG* 3.8 22.0 + - + +
180A LEU* 3.7 43.3 - - + +
181A GLY* 3.8 6.5 - - - +
186A MSE 3.9 39.0 - - + +
189A LEU* 4.7 4.0 - - + -
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Residues in contact with GLN 145 (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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134A SER 4.3 0.9 - - - -
135A LEU* 3.2 9.0 - - - +
136A ASN* 2.8 65.7 + - + +
138A LEU* 3.8 32.2 - - + +
143A GLN* 4.0 0.4 + - + -
144A LEU* 1.3 74.0 - - - +
146A MSE 1.3 61.3 + - - +
156A ILE* 3.5 40.5 + - + +
158A ASP* 3.3 20.5 + - - +
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Residues in contact with MSE 146 (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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133A LEU* 4.0 23.1 - - + -
134A SER 3.3 4.5 - - - -
135A LEU* 3.5 24.9 - - + -
144A LEU* 5.2 3.8 - - + -
145A GLN* 1.3 75.0 - - - +
147A GLY* 1.3 59.5 + - - +
156A ILE* 4.2 2.7 - - - -
158A ASP* 3.1 7.8 + - - -
159A VAL* 2.9 13.9 + - - +
173A LEU* 3.3 48.5 - - + +
176A VAL* 4.0 24.0 - - + -
177A ARG* 2.9 61.5 + - + +
180A LEU* 4.7 1.6 - - - -
192A VAL* 4.6 1.6 - - - -
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Residues in contact with GLY 147 (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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133A LEU* 3.5 12.0 - - - +
134A SER* 2.8 37.3 + - - +
146A MSE 1.3 76.8 - - - +
148A PHE* 1.3 65.5 + - - -
156A ILE* 3.7 7.3 - - - +
157A VAL 3.2 11.2 - - - -
159A VAL* 3.4 13.0 - - - -
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Residues in contact with PHE 148 (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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87A CYS* 3.7 29.6 - - - -
89A GLY* 5.4 2.2 - - - +
128A ARG* 6.3 0.7 - - - -
131A ALA* 4.2 19.1 - - + -
132A ARG 3.4 25.8 - - - -
133A LEU* 3.7 20.4 - - + -
134A SER* 5.0 2.2 - - - -
147A GLY* 1.3 78.1 - - - -
149A ARG* 1.3 64.4 + - - +
156A ILE* 3.4 6.1 - - - -
157A VAL* 2.9 31.6 + - - +
159A VAL* 3.5 24.8 - - + +
162A CYS* 3.9 28.7 - - + -
165A LEU* 5.3 2.7 - - + -
1432A SF4 4.0 9.9 - - - -
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Residues in contact with ARG 149 (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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87A CYS* 3.9 1.0 - - - -
88A GLY* 2.8 30.3 + - - -
134A SER* 4.8 11.9 + - - +
148A PHE* 1.3 78.4 - - - +
150A LYS* 1.3 56.4 + - - +
153A SER 3.5 27.3 + - - +
154A SER* 3.7 31.9 - - - +
155A ASP 3.4 6.3 - - - +
156A ILE* 4.6 2.5 - - + +
157A VAL* 4.5 0.2 - - - -
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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