Contacts of the strand formed by residues 264 - 274 (chain A) in PDB entry 4IBU
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 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A TYR* 3.1 22.4 + - - +
256A THR* 3.9 20.2 - - + -
257A LEU 3.9 2.0 - - - +
258A GLU* 4.7 11.4 - - + +
262A GLY 4.1 11.4 - - - +
263A ASN* 1.3 75.5 - - - +
265A LEU* 1.3 64.9 + - - +
266A GLY 3.4 26.5 - - - +
267A ARG* 3.7 26.7 - - - +
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Residues in contact with LEU 265 (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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103A TYR* 3.7 7.2 - - - -
104A GLN 4.1 0.9 - - - +
105A GLY* 3.4 23.6 - - - -
106A SER* 4.2 6.0 + - - +
107A TYR* 4.2 32.6 + - + -
151A PRO* 5.1 0.2 - - + -
152A PRO* 5.5 2.0 - - + -
155A THR* 4.1 20.2 - - + +
257A LEU* 2.8 24.0 + - + +
258A GLU 3.8 7.0 - - - +
259A ASP* 3.8 36.3 - - + +
263A ASN* 4.7 1.6 - - + +
264A LEU* 1.3 81.7 - - - +
266A GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 266 (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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103A TYR* 3.4 18.6 + - - -
104A GLN 4.3 3.8 - - - -
109A PHE* 3.8 16.8 - - - -
256A THR* 3.4 0.7 - - - -
257A LEU* 2.9 23.2 + - - +
264A LEU* 3.4 10.1 - - - +
265A LEU* 1.3 80.9 - - - +
267A ARG* 1.3 63.6 + - - +
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Residues in contact with ARG 267 (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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99A SER* 3.2 51.0 + - - +
100A GLN 3.9 7.2 - - - -
101A LYS* 3.0 33.1 + - - +
102A THR* 3.4 4.7 - - - +
103A TYR* 2.9 54.8 + - + +
109A PHE* 3.8 7.1 - - - +
254A ILE* 3.7 14.1 - - + +
255A ILE 3.3 4.7 - - - -
256A THR* 3.7 22.2 - - + +
264A LEU* 3.7 24.2 - - + +
266A GLY* 1.3 75.5 - - - +
268A ASN* 1.3 67.7 + - - +
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Residues in contact with ASN 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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102A THR* 3.8 24.9 + - - +
104A GLN* 6.3 0.2 - - - +
109A PHE* 4.2 9.7 + - + -
110A ARG* 4.3 10.3 - - - +
111A LEU* 3.3 50.2 - - + +
113A PHE* 5.3 1.9 - - - -
131A ASN* 5.2 2.4 + - - -
254A ILE* 3.6 3.3 - - - +
255A ILE 2.8 30.9 + - - +
267A ARG* 1.3 76.5 + - - +
269A SER* 1.3 84.1 + - - +
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Residues in contact with SER 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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100A GLN* 3.4 25.9 + - - +
102A THR* 3.9 9.4 + - - -
131A ASN* 3.0 17.7 + - - +
252A LEU* 5.0 10.1 - - - +
253A THR 3.1 15.0 - - - -
254A ILE* 4.2 13.7 - - - -
268A ASN* 1.3 88.4 + - - +
270A PHE* 1.3 69.5 + - - +
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Residues in contact with PHE 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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111A LEU* 3.8 10.5 - - + -
113A PHE* 3.7 26.0 - + + -
126A TYR* 4.5 1.8 - + + -
131A ASN* 3.6 25.8 - - - +
133A MET* 3.8 23.1 - - + -
143A VAL* 4.2 19.7 - - + -
234A TYR* 5.7 0.7 - + - -
236A TYR* 3.6 15.9 - - - -
252A LEU* 3.4 5.8 - - - -
253A THR* 2.8 41.6 + - + -
255A ILE* 3.8 25.8 - - + -
269A SER* 1.3 79.9 - - - +
271A GLU* 1.3 73.8 + - - +
272A VAL* 3.4 20.4 - - + -
304A EDO 4.7 0.9 - - - -
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Residues in contact with GLU 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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130A LEU* 4.7 2.3 - - - +
131A ASN 3.0 8.2 + - - +
132A LYS* 3.1 44.0 + - + +
133A MET 2.8 24.2 + - - -
164A LYS* 3.1 32.9 + - + +
250A PRO* 3.6 9.8 - - - +
251A ILE 3.3 16.4 - - - +
252A LEU* 3.7 9.5 - - + +
270A PHE* 1.3 76.6 - - - +
272A VAL* 1.3 66.3 + - - +
285A GLU* 5.1 2.5 - - - +
303A EDO 3.5 13.5 - - - +
304A EDO 3.5 18.5 + - - +
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Residues in contact with VAL 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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132A LYS* 4.5 0.9 - - - -
133A MET* 3.3 10.3 - - + +
135A CYS* 4.2 9.0 - - - -
236A TYR* 3.6 17.3 - - + +
240A SER* 4.0 1.2 + - - -
251A ILE* 3.0 29.5 + - + +
253A THR* 3.3 26.5 - - - +
270A PHE* 3.4 23.6 - - + +
271A GLU* 1.3 79.7 - - - +
273A CYS* 1.3 58.6 + - - +
274A VAL* 3.8 25.4 - - + -
303A EDO 2.3 26.8 + - - -
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Residues in contact with CYS 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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132A LYS* 3.7 13.4 - - - +
133A MET 2.9 7.5 + - - +
134A PHE* 3.3 18.2 - - + -
135A CYS* 3.0 24.8 + - - -
240A SER* 3.4 8.7 - - - -
272A VAL* 1.3 72.7 - - - +
274A VAL* 1.3 62.7 + - - +
275A CYS* 3.7 25.6 + - - -
281A ASP* 5.0 4.3 - - - -
303A EDO 3.6 27.4 - - - -
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Residues in contact with VAL 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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135A CYS* 3.2 12.8 - - - +
136A GLN 4.2 1.1 - - - -
137A LEU* 3.8 20.9 - - - +
194A LEU* 5.1 0.2 - - + -
236A TYR* 3.5 31.9 - - + -
238A CYS 3.2 26.0 - - - +
239A ASN* 3.6 16.0 - - - +
240A SER* 2.9 36.6 + - - +
246A MET* 4.8 6.5 - - + -
251A ILE* 5.4 2.2 - - + -
272A VAL* 3.8 17.3 - - + -
273A CYS* 1.3 70.1 - - - +
275A CYS* 1.3 64.0 + - - +
8F G 4.5 1.6 + - - -
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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