Contacts of the strand formed by residues 248 - 255 (chain A) in PDB entry 1B4V
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 HIS 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LEU* 3.9 11.3 - - + +
40A GLU 2.9 24.6 + - - -
41A MET* 3.2 2.4 + - - -
245A GLN* 3.6 45.1 + - + +
246A THR 2.6 25.4 + - - -
247A LEU* 1.3 77.3 - - - +
249A GLN* 1.3 59.5 + - - +
265A VAL* 3.8 22.2 - - + -
266A GLU 3.3 4.0 - - - -
267A GLN* 3.6 30.3 - - + +
278A LYS* 3.2 32.2 - - + -
280A ILE* 5.3 0.9 - - + -
510A FAD 3.5 6.2 - - - -
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Residues in contact with GLN 249 (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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41A MET* 3.6 37.4 - - + +
67A TRP* 5.9 0.6 - - - -
247A LEU 4.1 1.4 - - - -
248A HIS* 1.3 72.3 - - - +
250A VAL* 1.3 69.2 + - - +
251A LYS* 3.5 31.6 + - + +
265A VAL* 3.5 3.2 - - - -
266A GLU* 2.9 45.2 + - + +
268A LYS* 4.7 15.4 - - + +
296A GLU* 5.5 0.7 - - - +
396A ARG* 4.6 13.8 + - - +
510A FAD 3.5 23.5 + - + +
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Residues in contact with VAL 250 (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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16A ILE* 3.8 42.2 - - + -
39A LEU* 3.7 32.3 - - + -
249A GLN* 1.3 75.8 - - - +
251A LYS* 1.3 62.4 + - - +
252A THR 3.8 19.1 - - - +
253A ILE* 4.2 2.2 - - + -
263A LEU* 4.1 11.7 - - + -
264A THR 3.6 6.7 - - - +
265A VAL* 4.2 3.4 - - + +
297A LEU* 3.6 17.2 - - + +
300A ARG* 4.8 1.4 + - - -
510A FAD 3.0 30.6 + - - +
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Residues in contact with LYS 251 (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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249A GLN* 3.9 27.6 + - + +
250A VAL* 1.3 81.5 - - - +
252A THR* 1.3 66.2 + - + +
264A THR* 2.9 18.6 + - - +
266A GLU* 3.7 42.3 + - + +
297A LEU* 3.7 5.5 - - - +
300A ARG* 2.8 49.1 + - - +
395A ASP* 4.7 13.1 + - - -
396A ARG* 3.9 23.2 - - - +
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Residues in contact with THR 252 (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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250A VAL* 3.8 1.8 - - - +
251A LYS* 1.3 86.4 - - + +
253A ILE* 1.3 68.5 + - - +
254A ARG* 6.0 1.8 - - - +
262A ALA 4.6 0.6 + - - -
263A LEU* 3.3 8.8 - - - +
264A THR* 2.6 53.3 + - + +
297A LEU* 4.8 1.1 - - - -
300A ARG* 4.4 13.2 - - + +
304A THR* 6.0 1.6 - - - +
306A THR* 5.3 12.1 - - + -
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Residues in contact with ILE 253 (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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16A ILE* 4.1 18.4 - - + -
250A VAL* 4.2 5.6 - - + -
252A THR* 1.3 79.7 - - - +
254A ARG* 1.3 66.8 + - - +
261A TYR* 4.4 5.8 - - + -
262A ALA 3.6 2.9 - - - -
263A LEU* 3.6 15.3 - - + -
285A LEU* 3.5 22.4 - - + -
287A LEU* 4.2 17.7 - - + -
297A LEU* 4.0 30.4 + - + +
298A LEU* 4.7 7.9 - - + -
301A ALA* 3.9 5.9 - - + +
306A THR* 2.7 29.4 + - - -
307A LEU* 3.7 24.3 - - + +
470A LEU* 5.0 1.6 - - + -
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Residues in contact with ARG 254 (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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252A THR* 6.0 1.6 - - - +
253A ILE* 1.3 76.7 - - - +
255A GLN* 1.3 62.6 + - - +
256A THR* 3.8 27.3 - - - +
257A LYS* 4.9 4.2 - - - +
261A TYR* 3.3 11.9 - - - -
262A ALA* 2.9 54.0 + - + +
279A GLU* 3.5 24.2 + - - -
306A THR* 3.5 26.2 - - + +
307A LEU* 4.2 2.0 - - - -
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Residues in contact with GLN 255 (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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254A ARG* 1.3 82.3 + - - +
256A THR* 1.3 75.0 + - - +
257A LYS* 5.5 0.7 - - - +
259A GLY* 3.6 21.2 + - - -
260A GLY 3.3 14.1 - - - +
261A TYR* 3.4 30.2 + - + -
306A THR 3.7 7.1 + - - +
307A LEU* 3.9 8.4 - - + +
309A ASN* 5.4 2.6 + - - -
467A TYR* 3.4 22.6 - - + +
468A LYS* 4.9 4.8 + - - +
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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