Contacts of the strand formed by residues 267 - 277 (chain A) in PDB entry 1ASC
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 VAL 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A PHE* 3.8 18.8 - - + -
111A GLN* 5.6 1.3 - - + -
112A THR 4.2 0.2 - - - -
114A GLY* 3.6 9.1 - - - +
255A SER* 3.8 3.3 + - - -
256A TYR* 3.1 30.9 + - + -
257A SER* 3.9 6.4 + - - -
262A LEU* 3.9 22.9 - - + +
265A GLU* 3.9 6.7 - - + -
266A ARG* 1.3 76.2 - - - +
268A GLY* 1.3 58.7 + - - +
302A GLY* 3.6 27.8 - - - -
303A ALA* 3.7 28.0 - - + +
306A VAL* 3.8 10.1 - - + -
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Residues in contact with GLY 268 (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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86A PHE* 3.7 8.7 - - - -
111A GLN* 3.3 7.3 - - - +
112A THR* 2.9 36.4 + - - -
114A GLY 3.7 10.3 - - - -
254A SER 3.2 13.2 - - - -
255A SER* 4.1 2.5 - - - -
256A TYR* 4.6 3.4 - - - -
267A VAL* 1.3 75.7 - - - +
269A ALA* 1.3 62.1 + - - +
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Residues in contact with ALA 269 (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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86A PHE* 4.1 7.6 - - + -
90A THR* 3.5 24.5 - - + -
109A THR* 3.8 12.3 - - + -
110A ALA 3.2 5.6 - - - -
112A THR* 3.9 1.4 - - - +
118A ALA* 3.2 10.9 - - - +
252A VAL 3.6 0.3 - - - +
253A ALA* 3.4 0.9 - - - -
254A SER* 2.9 47.2 + - - +
256A TYR* 4.9 0.7 - - + -
268A GLY* 1.3 75.3 - - - +
270A CYS* 1.3 60.4 + - - +
271A THR* 4.0 2.2 - - - +
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Residues in contact with CYS 270 (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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109A THR* 3.4 0.5 - - - -
110A ALA* 2.7 37.9 + - + +
112A THR* 4.1 4.7 - - - +
118A ALA* 3.6 32.8 - - + +
121A VAL* 4.6 3.6 - - + -
122A ALA* 4.3 6.1 - - - -
251A ILE* 4.0 21.1 - - - -
252A VAL 3.4 4.9 - - - -
253A ALA* 5.3 0.4 - - - -
269A ALA* 1.3 73.8 - - - +
271A THR* 1.3 61.2 + - - +
287A MET* 3.4 37.0 - - + +
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Residues in contact with THR 271 (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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90A THR* 4.4 1.4 - - - +
91A GLN* 4.6 2.0 - - + -
94A LEU* 3.8 16.4 - - + +
95A PHE* 4.0 30.7 - - + -
107A ALA* 4.2 7.4 - - + -
108A ARG 3.3 5.8 - - - +
109A THR* 3.0 26.3 + - - +
250A LEU 4.7 0.2 - - - -
251A ILE* 3.2 10.0 - - - +
252A VAL* 2.8 44.4 + - + +
254A SER* 5.3 0.2 + - - -
269A ALA* 4.0 1.4 - - - +
270A CYS* 1.3 73.9 + - - +
272A LEU* 1.3 70.6 + - - +
273A VAL* 4.6 1.3 - - + -
287A MET* 4.4 1.1 - - - -
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Residues in contact with LEU 272 (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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107A ALA* 3.1 6.4 - - - +
108A ARG 2.9 31.3 + - - +
125A PHE* 3.8 28.5 - - + -
250A LEU 3.7 1.8 - - - +
251A ILE* 3.9 18.6 - - + -
271A THR* 1.3 74.5 - - - +
273A VAL* 1.3 68.5 + - - +
274A ALA* 5.2 1.6 - - + -
280A VAL* 3.6 16.9 - - + +
283A ALA* 3.6 15.7 - - + +
284A PHE* 3.4 38.8 - - + +
287A MET* 3.8 18.6 - - + -
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Residues in contact with VAL 273 (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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95A PHE* 4.1 6.1 - - + -
101A LEU* 3.6 31.9 - - + -
106A ARG* 3.0 36.6 - - - +
107A ALA* 4.1 9.0 - - + -
247A HIS 4.4 1.3 - - - +
248A LYS 3.4 9.9 - - - +
249A GLU* 3.4 5.0 - - - +
250A LEU* 2.8 55.5 + - + +
271A THR* 4.6 1.8 - - + -
272A LEU* 1.3 81.1 - - - +
274A ALA* 1.4 60.9 + - - +
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Residues in contact with ALA 274 (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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106A ARG 3.1 10.5 + - - -
248A LYS 3.4 4.9 - - - -
249A GLU* 3.2 23.0 - - + +
272A LEU* 5.2 2.0 - - + -
273A VAL* 1.4 76.1 - - - +
275A ALA* 1.4 66.1 + - - +
276A ASP 3.5 2.7 - - - -
279A THR* 3.6 18.4 - - + +
280A VAL* 3.4 35.4 - - + +
283A ALA* 5.0 6.5 - - + -
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Residues in contact with ALA 275 (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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106A ARG* 3.0 28.1 + - - +
248A LYS* 3.0 38.2 + - + +
249A GLU* 5.1 0.9 - - - +
274A ALA* 1.4 79.0 - - - +
276A ASP* 1.3 72.1 + - - +
279A THR* 5.0 1.1 - - + +
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Residues in contact with ASP 276 (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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104A ASP 5.4 0.2 - - - -
106A ARG* 4.1 12.5 - - - +
274A ALA 3.5 0.4 - - - -
275A ALA* 1.3 89.0 + - - +
277A SER* 1.3 66.9 + - - +
278A GLU* 3.5 13.1 + - + +
279A THR* 2.6 41.4 + - - -
280A VAL* 3.2 22.7 + - - +
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Residues in contact with SER 277 (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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104A ASP 4.0 8.8 + - - -
105A LYS* 3.2 45.3 + - - +
276A ASP* 1.3 72.9 - - - +
278A GLU* 1.3 62.7 + - - +
280A VAL* 3.0 3.7 - - - +
281A ASP* 2.7 41.8 + - - +
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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