Contacts of the strand formed by residues 259 - 265 (chain A) in PDB entry 3NDK
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 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A VAL* 3.9 21.3 - - - +
253A ILE 3.2 14.4 - - - -
254A GLU* 4.1 12.3 - - - -
255A ASN* 4.4 3.8 - - - +
258A GLY* 1.3 75.8 - - - -
260A ARG* 1.3 61.4 - - - +
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Residues in contact with ARG 260 (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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219A GLU* 4.5 6.1 + - - +
220A SER* 3.6 26.3 - - - +
252A VAL* 3.6 4.1 - - - +
253A ILE* 2.8 43.9 + - + +
255A ASN* 5.6 3.8 - - - +
259A SER* 1.3 75.6 - - - +
261A GLU* 1.3 65.6 + - - +
262A ILE* 3.5 24.0 - - - +
275A ASP* 5.3 5.9 + - - -
2T C 2.8 60.7 + - - +
3T A 5.7 0.2 - - - +
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Residues in contact with GLU 261 (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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126A PRO* 6.1 0.9 - - - +
127A SER* 4.9 14.7 - - - -
220A SER* 5.2 3.1 - - - +
224A PRO* 4.7 11.6 - - - +
250A VAL* 3.6 29.5 - - + +
251A LYS 3.4 4.7 - - - +
252A VAL* 4.3 16.7 - - + +
260A ARG* 1.3 81.4 + - - +
262A ILE* 1.3 67.4 + - - +
263A ILE* 5.8 1.6 - - + -
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Residues in contact with ILE 262 (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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219A GLU* 3.6 41.3 - - + +
220A SER* 4.9 0.2 - - - -
224A PRO* 5.1 1.8 - - - -
250A VAL* 3.4 5.9 - - - +
251A LYS* 2.8 57.3 + - + +
253A ILE* 4.1 17.7 - - + -
260A ARG* 3.5 27.1 - - - +
261A GLU* 1.3 78.5 - - - +
263A ILE* 1.3 68.2 + - - +
264A THR* 4.7 6.1 - - - +
2T C 3.6 26.9 - - - +
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Residues in contact with ILE 263 (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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219A GLU* 4.9 5.5 + - - +
223A ILE* 4.2 15.7 - - + +
224A PRO* 3.8 28.7 - - + +
227A TYR* 4.0 35.7 - - + -
228A ASN* 4.7 11.0 - - - +
248A THR* 4.1 8.7 - - - -
249A ARG 3.7 4.0 - - - +
250A VAL* 3.8 29.4 - - + -
261A GLU* 5.8 1.6 - - + -
262A ILE* 1.3 82.7 - - - +
264A THR* 1.3 67.9 + - - +
265A LEU* 3.5 29.8 + - + +
270A VAL* 5.6 3.8 - - - +
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Residues in contact with THR 264 (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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9A GLU* 5.6 3.1 - - - +
248A THR* 3.2 10.7 - - - -
249A ARG* 2.8 43.6 + - - +
251A LYS* 3.7 28.6 - - - +
262A ILE* 4.0 5.6 + - - +
263A ILE* 1.3 72.0 - - - +
265A LEU* 1.3 66.0 + - - +
266A PHE* 3.7 22.6 + - + -
356A GLN* 6.3 0.9 - - - +
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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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9A GLU* 4.2 1.0 - - - +
205A TRP* 4.5 5.4 - - + -
213A LEU* 4.2 17.0 - - + -
223A ILE* 4.0 22.4 - - + -
227A TYR* 4.7 4.0 - - + -
242A LEU* 4.1 26.7 - - + +
243A SER* 4.6 1.6 - - - -
247A LYS 4.2 2.9 - - - -
248A THR* 3.8 20.4 - - + -
263A ILE* 3.5 22.4 + - + +
264A THR* 1.3 74.5 - - - +
266A PHE* 1.3 66.2 + - - +
267A GLY 3.4 0.3 + - - -
268A ILE* 3.2 52.4 + - + +
270A VAL* 4.8 8.6 - - + +
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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