Contacts of the strand formed by residues 129 - 137 (chain A) in PDB entry 1A9R
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 ILE 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A GLY 3.7 8.3 + - - +
128A ASP* 1.3 77.9 + - - +
130A MET* 1.3 61.6 + - - +
178A TRP* 3.9 27.6 - - + -
186A GLU 4.8 1.3 + - - +
187A LEU* 3.5 22.9 - - + +
188A GLN* 3.1 26.4 + - - +
238A PHE* 4.1 27.4 - - + -
239A SER 3.5 4.0 - - - +
240A LEU* 4.3 5.6 - - + -
270A LYS* 4.1 19.5 - - + +
271A LEU* 3.6 31.9 - - + -
274A PHE* 4.5 13.0 - - + -
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Residues in contact with MET 130 (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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124A PHE* 3.5 30.5 - - + -
128A ASP 4.1 0.4 - - - -
129A ILE* 1.3 75.2 - - - +
131A LEU* 1.3 66.4 + - - +
132A ILE* 3.4 9.9 + - + -
188A GLN* 3.6 8.3 - - + -
189A GLU* 3.8 6.7 - - - +
190A GLY* 3.5 46.7 - - - +
191A THR 4.2 7.2 - - - -
192A TYR* 4.3 2.7 - - + -
215A ASP* 3.9 8.1 - - - -
216A ALA* 3.9 21.1 - - + -
238A PHE* 3.2 3.8 - - - -
239A SER* 2.8 51.9 + - - +
241A ILE* 4.5 8.5 - - + -
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Residues in contact with LEU 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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129A ILE 4.1 0.6 - - - -
130A MET* 1.3 71.5 - - - +
132A ILE* 1.3 62.2 + - - +
133A ARG 3.2 0.3 + - - -
171A ARG* 3.9 25.4 - - + +
174A ALA* 3.7 8.7 - - + -
175A HIS* 3.4 35.4 - - + +
187A LEU* 3.5 29.2 - - + -
188A GLN 2.9 14.1 + - - +
189A GLU* 3.3 9.4 - - + +
190A GLY 3.0 25.3 + - - -
236A PHE* 3.6 33.0 - - + -
237A GLY 3.9 2.7 - - - +
238A PHE* 4.0 7.6 - - + -
274A PHE* 4.6 4.7 - - + -
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Residues in contact with ILE 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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113A VAL* 5.1 0.9 - - + +
115A ASN* 4.0 13.2 - - - +
130A MET* 4.2 7.6 - - + +
131A LEU* 1.3 70.5 - - - +
133A ARG* 1.3 58.0 + - - +
134A ASP 3.4 22.0 - - - +
166A TYR* 3.5 47.9 - - + +
171A ARG* 3.6 8.9 - - - +
190A GLY 3.7 4.0 - - - +
192A TYR* 4.1 16.4 - - + -
221A THR* 4.5 14.8 - - + -
237A GLY* 3.0 20.8 + - - +
238A PHE* 3.8 21.3 - - - +
239A SER* 3.9 20.2 - - - +
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Residues in contact with ARG 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 LEU 3.2 1.2 + - - -
132A ILE* 1.3 73.7 - - - +
134A ASP* 1.3 64.7 + - + +
166A TYR* 3.8 14.5 + - - +
171A ARG* 4.0 29.1 + - - +
189A GLU* 3.7 43.1 + - + +
190A GLY* 2.8 28.0 + - - +
191A THR* 3.6 21.8 + - - +
215A ASP* 3.9 6.1 + - - -
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Residues in contact with ASP 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 ILE* 3.4 9.2 - - - +
133A ARG* 1.3 86.3 - - + +
135A HIS* 1.3 79.8 + - - +
162A MET 5.0 7.1 - - - +
163A SER* 5.5 5.3 - - - +
166A TYR* 3.9 12.9 - - - -
190A GLY 3.5 1.6 + - - -
191A THR* 3.3 20.5 + - - +
192A TYR 3.0 20.4 + - - -
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Residues in contact with HIS 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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134A ASP* 1.3 90.1 + - - +
136A ILE* 1.3 67.9 + - - +
137A ASN* 4.1 11.2 - - + +
162A MET* 4.9 11.3 - - + +
165A ALA* 4.9 6.7 - - + -
166A TYR* 2.7 36.5 + + - +
191A THR* 4.2 1.3 - - - -
192A TYR* 3.0 17.3 - - + +
222A VAL* 3.7 39.2 - - + +
225A VAL* 4.3 13.7 - - + -
226A ILE* 4.0 19.5 - - + +
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Residues in contact with ILE 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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135A HIS* 1.3 78.5 - - - +
137A ASN* 1.3 61.9 + - - +
138A LEU* 3.7 19.5 + - + -
141A PHE* 4.5 13.7 - - + -
191A THR* 3.7 21.8 - - + -
192A TYR 2.8 6.3 + - - +
193A VAL* 3.9 17.9 - - + +
194A MET* 3.1 25.8 + - - +
212A LEU* 3.9 30.7 - - + +
213A GLY 4.7 0.7 - - - -
214A ALA* 4.3 17.5 - - + +
222A VAL* 4.6 2.1 - - - +
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Residues in contact with ASN 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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93A PHE* 5.6 2.4 - - - -
135A HIS* 4.1 8.6 - - + +
136A ILE* 1.3 74.9 - - - +
138A LEU* 1.3 62.3 + - - +
139A PRO* 3.3 22.4 - - - +
140A GLY* 3.1 27.7 + - - +
141A PHE* 3.3 22.0 + - + -
144A GLU 4.6 3.0 + - - +
145A ASN* 4.7 6.6 + - - -
146A PRO* 5.8 1.6 - - - +
194A MET* 4.5 5.8 - - - +
222A VAL* 3.6 32.1 - - + +
223A PRO* 5.6 1.6 - - - +
226A ILE* 4.7 11.8 - - + +
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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