Contacts of the strand formed by residues 175 - 182 (chain A) in PDB entry 1AXS
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 LEU 175 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 3.1 7.6 - - - +
136A LEU* 2.8 62.0 + - + -
139A PHE* 3.6 20.6 - - + -
142A ARG 5.7 2.0 - - - +
144A ALA* 5.3 8.3 - - + +
146A VAL* 4.1 5.2 - - + -
161A GLU* 2.9 37.5 - - - +
162A SER 3.5 9.2 - - - +
163A VAL* 3.9 20.0 - - + -
174A SER* 1.3 76.7 - - - +
176A SER* 1.3 75.3 + - - +
177A SER* 4.0 2.0 - - - +
166B PHE* 3.6 4.3 - - - -
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Residues in contact with SER 176 (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 VAL* 5.0 5.8 - - - -
134A CYS 3.3 8.1 - - - -
135A LEU* 5.2 0.9 - - - -
160A GLN 3.7 0.9 + - - +
161A GLU* 3.2 6.1 - - - +
162A SER* 3.0 39.8 + - - -
175A LEU* 1.3 78.8 - - - +
177A SER* 1.3 59.9 + - - +
178A THR* 4.0 11.5 + - - -
166B PHE* 3.6 30.6 - - - +
179B SER* 4.7 9.3 - - - -
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Residues in contact with SER 177 (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 VAL* 3.5 2.8 - - - +
134A CYS* 2.8 39.0 + - - -
146A VAL* 3.9 24.3 + - - +
148A TRP* 3.1 30.2 + - - -
159A SER* 4.4 5.4 - - - -
160A GLN 3.5 3.9 + - - -
161A GLU* 3.9 20.1 - - - +
175A LEU* 4.0 2.4 - - - +
176A SER* 1.3 72.6 - - - +
178A THR* 1.3 63.5 + - - +
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Residues in contact with THR 178 (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 SER* 4.0 21.5 - - - +
132A VAL 3.4 7.9 - - - +
133A VAL* 4.2 20.0 - - + +
148A TRP* 4.5 1.1 - - - -
158A ASN 3.7 0.9 - - - +
159A SER* 3.2 4.9 - - - -
160A GLN* 2.8 46.9 + - - +
176A SER* 4.0 10.6 + - - -
177A SER* 1.3 77.5 + - - +
179A LEU* 1.3 62.6 + - - +
180A THR* 4.0 7.4 + - - +
141B LEU* 4.8 7.9 - - + +
143B LYS* 5.1 4.9 - - - +
169B VAL* 6.4 1.3 - - - -
179B SER* 4.8 5.2 + - - -
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Residues in contact with LEU 179 (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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130A ALA 3.5 0.9 - - - +
131A SER* 3.2 5.2 - - - -
132A VAL* 2.7 56.6 + - + +
148A TRP* 3.7 44.6 - - + +
150A VAL* 4.1 23.1 - - + -
155A GLN* 4.2 6.3 - - + -
158A ASN* 3.0 50.7 - - + +
159A SER* 4.3 2.2 - - - +
177A SER 4.2 0.4 - - - -
178A THR* 1.3 70.7 - - - +
180A THR* 1.3 63.2 + - - +
181A LEU* 4.3 10.3 - - + -
192A TYR* 4.6 3.4 - - + -
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Residues in contact with THR 180 (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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129A THR* 3.6 28.5 - - + -
130A ALA 3.3 3.6 - - - +
131A SER* 3.1 17.5 + - - +
158A ASN* 3.1 28.3 + - - +
160A GLN* 5.5 3.4 + - - -
178A THR* 4.1 8.0 + - - +
179A LEU* 1.3 75.0 - - - +
181A LEU* 1.3 70.6 + - - +
143B LYS* 3.7 15.8 + - - +
171B GLN* 5.4 1.3 - - - +
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Residues in contact with LEU 181 (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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129A THR* 3.9 2.2 - - - +
130A ALA* 2.7 55.0 + - + +
132A VAL* 4.7 10.5 - - + -
150A VAL* 5.0 4.3 - - + -
155A GLN* 4.6 7.6 - - - +
158A ASN* 4.3 17.5 - - - +
179A LEU* 4.6 12.6 - - + +
180A THR* 1.3 82.6 - - - +
182A SER* 1.3 63.7 + - - +
185A ASP* 4.4 23.8 - - + +
186A TYR* 4.3 15.3 - - + -
189A HIS* 6.1 0.9 - - + -
192A TYR* 4.9 10.8 - - + -
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Residues in contact with SER 182 (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 GLY 3.1 14.6 - - - -
129A THR* 4.4 0.4 - - - +
130A ALA* 4.2 0.9 - - - -
181A LEU* 1.3 81.3 - - - +
183A LYS* 1.3 65.9 + - - +
184A ALA* 4.2 6.8 - - - +
185A ASP* 3.2 29.0 + - - +
186A TYR* 3.2 21.0 + - - +
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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