Contacts of the strand formed by residues 234 - 244 (chain A) in PDB entry 1A9Q
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 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLN* 4.7 1.6 + - - -
109A GLU* 3.0 22.0 + - - +
110A THR* 2.8 38.4 + - + +
111A LEU 2.9 26.5 + - - +
167A ASP* 3.8 29.4 + - + +
170A MET* 3.6 28.1 - - - -
229A ARG* 4.0 7.6 - - - +
232A GLY 3.8 1.8 + - - -
233A LEU* 1.3 71.8 - - - +
235A VAL* 1.3 62.1 + - - +
282A ILE* 5.2 11.2 + - - +
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Residues in contact with VAL 235 (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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111A LEU* 3.5 15.3 - - + +
113A VAL* 4.5 4.5 - - + -
165A ALA 3.6 14.9 + - - +
166A TYR* 3.8 9.3 - - + -
167A ASP* 3.0 33.5 + - - +
225A VAL* 4.1 29.2 - - + +
228A ALA* 3.6 27.6 - - + -
229A ARG* 3.9 11.7 - - + +
233A LEU 3.4 12.7 + - - +
234A ARG* 1.3 80.5 - - - +
236A PHE* 1.3 71.6 + - - +
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Residues in contact with PHE 236 (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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110A THR* 5.5 2.7 - - + -
111A LEU 3.0 8.4 + - - +
112A VAL* 3.0 31.4 - - + -
113A VAL* 2.8 23.7 + - - +
131A LEU* 3.9 18.2 - - + -
166A TYR* 5.0 2.5 - - - +
167A ASP 5.3 0.7 - - - +
170A MET* 3.6 41.5 - - + -
171A ARG* 4.4 13.0 - - + -
174A ALA* 3.9 19.1 - - + -
235A VAL* 1.3 79.6 - - - +
237A GLY* 1.3 63.6 + - - +
238A PHE* 3.5 37.5 - + - -
274A PHE* 5.0 0.2 - + - -
278A LEU* 3.7 27.6 - - + -
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Residues in contact with GLY 237 (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* 2.9 24.0 - - - -
131A LEU* 3.8 2.3 - - - -
132A ILE* 3.0 30.3 + - - +
166A TYR* 4.6 7.4 - - - -
171A ARG* 5.8 0.5 - - - +
236A PHE* 1.3 89.4 - - - +
238A PHE* 1.3 67.7 + - - +
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Residues in contact with PHE 238 (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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35A LEU* 4.5 0.7 - - + -
112A VAL* 4.5 2.7 - - + -
113A VAL 3.0 4.6 + - - -
114A THR* 3.2 36.3 - - + -
115A ASN* 3.2 22.4 + - - -
129A ILE* 4.1 20.4 - - + -
130A MET 3.2 16.2 - - - +
131A LEU* 3.9 8.5 - - + -
132A ILE* 3.7 7.7 - - - +
236A PHE* 3.5 35.4 - + - -
237A GLY* 1.3 73.7 - - - +
239A SER* 1.3 66.8 + - - +
240A LEU* 5.2 0.7 - - - -
271A LEU* 4.4 25.6 - - + -
274A PHE* 4.4 16.4 - + - -
275A VAL* 3.4 28.9 - - + -
278A LEU* 4.7 1.1 - - + -
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Residues in contact with SER 239 (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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115A ASN* 2.8 30.8 + - - +
117A ALA* 3.7 15.3 - - - -
129A ILE* 3.5 4.9 - - - +
130A MET* 2.9 44.9 + - - +
132A ILE* 3.8 7.8 - - - +
192A TYR* 3.6 15.9 - - - -
238A PHE* 1.3 78.2 - - - +
240A LEU* 1.3 60.9 + - - +
241A ILE* 3.6 5.3 + - - -
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Residues in contact with LEU 240 (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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33A SER* 3.6 28.9 - - - +
34A GLY 4.2 0.2 - - - +
115A ASN 2.8 14.7 + - - +
116A ALA* 3.4 2.4 - - - -
117A ALA 2.9 23.7 + - - -
127A GLY* 4.0 13.9 - - - +
128A ASP 3.7 12.8 - - - +
129A ILE* 4.4 3.4 - - + +
238A PHE* 5.2 1.7 - - + -
239A SER* 1.3 71.8 - - - +
241A ILE* 1.3 59.4 + - - +
242A THR* 3.0 17.7 + - + -
263A ALA* 4.1 5.8 - - + +
264A GLY* 3.7 26.5 - - - +
267A ALA* 3.8 22.2 - - + -
271A LEU* 3.9 24.0 - - + -
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Residues in contact with ILE 241 (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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117A ALA* 3.5 9.9 - - + +
119A GLY* 3.9 14.4 - - - +
124A PHE* 3.8 37.0 - - + -
125A GLU 3.9 19.3 - - - +
126A VAL* 3.6 0.9 - - - -
127A GLY* 2.9 26.3 + - - -
128A ASP* 2.8 30.4 + - + +
130A MET* 4.4 12.1 - - + -
216A ALA* 4.1 22.0 - - + -
239A SER* 4.5 4.7 - - - +
240A LEU* 1.3 69.8 - - - +
242A THR* 1.3 59.0 + - - +
243A ASN 3.7 20.9 - - - +
244A LYS* 5.2 1.6 - - + -
263A ALA* 4.9 0.3 - - - +
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Residues in contact with THR 242 (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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33A SER* 5.3 0.4 - - - -
116A ALA* 3.6 17.7 - - + -
117A ALA 3.0 8.9 + - - -
126A VAL* 3.6 13.9 - - - +
240A LEU* 3.0 34.7 + - + +
241A ILE* 1.3 72.5 - - - +
243A ASN* 1.3 75.5 + - - +
259A GLU* 4.1 10.2 - - - +
260A VAL* 3.7 29.2 - - + +
263A ALA* 3.6 17.2 - - + +
264A GLY* 4.5 1.1 - - - +
290A HPA 3.6 13.5 - - - -
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Residues in contact with ASN 243 (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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118A GLY* 3.5 2.8 - - - -
119A GLY 2.8 24.3 + - - -
126A VAL* 4.1 10.1 - - - -
241A ILE* 3.4 8.2 + - - +
242A THR* 1.3 85.9 + - - +
244A LYS* 1.3 72.7 + - - +
245A VAL* 4.4 1.8 - - - +
255A ALA* 3.9 18.7 - - - +
259A GLU* 3.6 26.5 - - + +
260A VAL* 3.7 7.4 - - + +
290A HPA 2.9 45.4 + - - -
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Residues in contact with LYS 244 (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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119A GLY* 3.9 8.5 - - - +
121A ASN 5.8 0.7 - - - -
122A PRO* 4.8 11.0 + - - -
124A PHE* 3.4 24.0 - - + +
125A GLU* 3.5 32.3 + - - +
126A VAL* 4.2 19.7 - - + +
241A ILE* 5.2 2.7 - - + -
243A ASN* 1.3 83.5 + - - +
245A VAL* 1.3 66.3 + - - +
246A ILE* 3.7 6.8 + - - +
255A ALA* 5.9 0.5 - - - +
259A GLU* 5.3 1.1 + - - +
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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