Contacts of the strand formed by residues 296 - 302 (chain A) in PDB entry 2I3T
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 SER 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A ASN* 4.4 0.9 - - - -
270A GLY 4.1 0.2 - - - -
271A SER* 3.0 41.2 + - - +
273A GLY* 4.3 0.4 - - - -
295A ASP* 1.3 75.0 - - - +
297A VAL* 1.3 59.9 + - - +
298A VAL* 3.3 7.0 + - - +
311A THR* 3.0 5.6 - - - -
312A SER 3.0 30.5 + - - +
313A ASP* 5.2 0.2 - - - +
314A ASP* 2.6 37.4 + - - -
317A LYS* 4.2 1.0 + - - -
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Residues in contact with VAL 297 (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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255A ASN* 3.1 18.1 + - - +
269A ALA* 3.3 32.0 - - + +
270A GLY 3.2 11.5 + - - +
273A GLY* 3.4 33.0 - - - +
274A ILE 3.9 7.4 - - - +
275A ILE* 3.8 14.6 - - + -
292A PHE* 4.2 14.6 - - + -
296A SER* 1.3 69.6 - - - +
298A VAL* 1.3 60.7 + - - +
299A LYS 4.2 0.7 - - - +
300A ILE* 3.9 11.2 - - + -
309A LEU* 4.0 6.5 - - + -
310A ALA 3.5 12.3 - - - +
311A THR* 4.3 7.6 - - + -
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Residues in contact with VAL 298 (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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13A TYR* 3.2 49.6 - - + +
14A ILE 3.6 12.3 - - - +
15A SER* 5.7 0.2 - - - -
197A ARG* 5.5 2.0 - - - +
255A ASN* 3.8 18.0 - - + +
256A SER* 3.8 10.8 - - - -
296A SER* 3.3 17.7 + - - +
297A VAL* 1.3 75.5 - - - +
299A LYS* 1.3 66.6 + - + +
310A ALA* 3.0 10.0 + - + +
312A SER* 4.0 20.4 - - - +
314A ASP* 4.3 7.0 - - - +
382B GLU* 5.9 0.2 - - - +
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Residues in contact with LYS 299 (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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14A ILE* 4.9 4.5 - - + +
15A SER 4.0 23.3 + - - +
16A ASP* 3.4 28.5 - - - -
17A ILE* 3.8 25.1 - - + +
18A LYS* 5.5 0.7 - - - +
106A ARG* 3.9 29.2 - - - +
198A ASP* 5.2 0.2 + - - -
255A ASN 5.2 1.6 + - - -
256A SER* 3.7 18.7 + - - +
297A VAL* 3.6 1.6 - - - +
298A VAL* 1.3 87.5 + - + +
300A ILE* 1.3 88.8 + - - +
309A LEU* 3.2 2.1 - - - +
310A ALA* 2.9 34.0 + - + +
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Residues in contact with ILE 300 (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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17A ILE* 5.0 1.2 - - - +
256A SER* 3.3 30.2 + - - +
258A GLU* 3.4 23.7 - - + +
267A TYR* 3.3 44.2 - - + +
268A THR 4.3 1.6 - - - +
269A ALA* 3.6 21.1 - - + -
275A ILE* 3.6 25.4 - - + -
297A VAL* 3.9 0.7 - - + -
299A LYS* 1.3 91.9 - - - +
301A ALA* 1.3 60.5 + - - +
302A CYS* 5.2 2.5 - - - -
307A LEU* 4.4 7.4 - - + -
308A CYS 3.3 7.2 - - - +
309A LEU* 3.9 3.8 - - + -
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Residues in contact with ALA 301 (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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17A ILE* 3.6 40.6 - - + +
18A LYS* 4.7 1.6 - - + +
19A ILE* 3.8 18.0 - - + +
258A GLU* 3.6 8.5 - - - +
300A ILE* 1.3 74.7 - - - +
302A CYS* 1.3 63.1 + - - +
307A LEU* 3.3 5.4 - - - +
308A CYS 2.9 31.5 + - - +
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Residues in contact with CYS 302 (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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19A ILE* 4.0 4.9 - - - +
258A GLU* 2.7 39.5 + - + +
259A PHE 4.0 10.0 - - - +
260A SER* 4.2 4.0 - - - -
261A PRO* 4.3 7.9 - - - +
267A TYR* 4.1 26.9 - - - -
300A ILE* 5.2 1.6 - - - -
301A ALA* 1.3 79.4 - - - +
303A SER* 1.3 59.9 + - - +
306A ILE 3.8 2.5 - - - -
307A LEU* 4.1 18.4 - - - -
339A TYR* 3.5 17.0 - - - +
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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