Contacts of the helix formed by residues 290 - 303 (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 GLY 290 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A GLY 3.2 4.8 + - - -
289A ALA* 1.3 75.6 - - - +
291A SER* 1.3 67.1 + - - -
292A LEU 3.2 3.1 - - - -
294A SER* 2.9 25.5 + - - -
474A ASP* 2.7 16.8 + - - +
510A FAD 3.5 28.5 - - - -
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Residues in contact with SER 291 (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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290A GLY* 1.3 70.4 - - - +
292A LEU* 1.3 57.9 + - - +
295A THR* 2.6 30.8 + - - -
318A TRP* 3.2 23.6 + - - -
388A PHE* 4.3 2.1 - - - -
448A PRO* 3.4 37.0 - - - +
450A GLY 2.9 19.0 + - - +
475A GLY* 4.1 0.9 - - - -
476A SER* 3.7 22.7 - - - +
510A FAD 4.3 3.4 + - - -
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 3.8 23.1 - - + -
101A TYR* 3.6 26.3 + - + +
106A VAL* 3.7 39.5 - - + -
108A VAL* 3.9 15.3 - - + -
110A ARG* 5.3 3.4 - - - +
290A GLY 3.2 0.6 - - - -
291A SER* 1.3 78.4 - - - +
293A GLY* 1.3 59.9 + - - +
295A THR* 4.0 1.0 - - - -
296A GLU* 3.0 31.8 + - - +
318A TRP* 4.3 8.5 - - - +
388A PHE* 3.4 30.1 - - + -
448A PRO* 4.3 3.6 - - + -
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Residues in contact with GLY 293 (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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110A ARG* 5.9 1.7 - - - +
289A ALA* 3.1 30.0 + - - -
292A LEU* 1.3 77.6 - - - +
294A SER* 1.3 63.1 + - - +
296A GLU* 3.5 8.0 + - - +
297A LEU* 3.1 28.4 + - - +
510A FAD 4.1 10.0 + - - -
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Residues in contact with SER 294 (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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287A LEU* 3.6 26.9 - - - +
289A ALA* 3.1 16.0 + - - +
290A GLY 2.9 16.0 + - - -
293A GLY* 1.3 69.0 - - - -
295A THR* 1.3 66.6 + - - +
297A LEU* 3.3 3.8 + - - +
298A LEU* 3.1 28.9 + - - +
452A CYS* 5.8 0.9 - - - -
472A VAL* 4.5 4.9 - - - -
474A ASP* 2.7 25.0 + - - -
476A SER* 3.9 12.8 - - - -
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Residues in contact with THR 295 (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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291A SER 2.6 25.7 + - - -
292A LEU 3.6 1.9 + - - -
293A GLY 3.4 0.4 - - - -
294A SER* 1.3 78.6 - - - +
296A GLU* 1.3 57.6 + - - +
298A LEU* 3.3 4.9 + - - +
299A VAL* 2.9 34.4 + - + +
314A VAL* 5.3 1.1 - - + -
315A GLY* 3.6 20.6 - - - +
388A PHE* 3.6 27.4 - - + -
451A GLY* 3.3 37.9 - - - +
452A CYS* 4.0 2.9 + - - -
476A SER* 3.7 6.8 - - - -
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Residues in contact with GLU 296 (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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101A TYR* 6.2 0.2 - - - -
249A GLN* 5.5 0.7 - - - +
292A LEU 3.0 20.4 + - - +
293A GLY* 3.8 7.1 - - - +
294A SER 3.3 0.2 - - - -
295A THR* 1.3 76.9 - - - +
297A LEU* 1.3 62.3 + - + +
299A VAL* 3.2 9.0 - - - +
300A ARG* 3.0 42.0 + - + +
388A PHE* 5.8 0.2 - - - -
390A TYR* 6.0 0.4 - - + -
396A ARG* 2.7 40.7 + - - -
397A ALA* 3.0 40.8 + - + +
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Residues in contact with LEU 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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16A ILE* 3.9 32.1 - - + -
250A VAL* 3.6 29.4 - - + +
251A LYS 3.7 21.1 - - - +
252A THR* 4.8 0.4 - - - -
253A ILE* 4.0 20.1 + - + +
287A LEU* 4.4 7.2 - - + -
289A ALA* 4.4 5.8 - - + -
293A GLY 3.1 21.4 + - - +
294A SER 3.6 4.7 - - - +
295A THR 3.3 0.2 - - - -
296A GLU* 1.3 75.8 - - + +
298A LEU* 1.3 59.4 + - - +
300A ARG* 3.6 11.2 - - - +
301A ALA* 3.0 28.4 + - - +
510A FAD 4.0 17.0 - - - +
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Residues in contact with LEU 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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253A ILE* 4.7 4.0 - - + -
287A LEU* 3.8 16.8 - - + -
294A SER 3.1 16.7 + - - +
295A THR* 3.9 2.0 - - - +
297A LEU* 1.3 75.7 - - - +
299A VAL* 1.3 60.7 + - - +
300A ARG 3.2 1.3 - - - -
301A ALA* 4.3 0.4 - - - -
302A ARG* 2.9 25.6 + - - +
307A LEU* 4.2 23.6 - - + -
310A LEU* 3.1 20.0 - - + +
314A VAL* 3.6 20.0 - - + -
452A CYS* 3.6 31.9 - - + -
464A VAL* 4.3 13.0 - - + -
470A LEU* 4.8 8.7 - - + -
472A VAL* 3.8 16.2 - - + -
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Residues in contact with VAL 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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295A THR* 2.9 30.5 + - + +
296A GLU* 3.2 14.1 - - - +
298A LEU* 1.3 71.5 - - - +
300A ARG* 1.3 65.6 + - - +
302A ARG* 4.2 13.0 - - - +
303A ASP* 3.0 29.8 + - - +
314A VAL* 3.8 14.6 - - + +
315A GLY* 3.8 28.9 - - - -
388A PHE* 4.0 11.2 - - + +
390A TYR* 4.0 16.6 - - + +
397A ALA* 3.7 19.5 - - + -
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Residues in contact with ARG 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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250A VAL 4.8 1.2 + - - -
251A LYS* 2.8 51.7 + - - +
252A THR* 4.4 14.4 - - + +
296A GLU* 3.0 36.0 + - - +
297A LEU* 3.6 19.1 - - - +
299A VAL* 1.3 79.2 - - - +
301A ALA* 1.3 53.1 + - - +
304A THR* 2.7 48.4 + - + +
390A TYR* 3.8 21.9 - - + +
395A ASP* 2.8 53.8 + - - +
396A ARG* 3.8 19.6 - - - +
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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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253A ILE* 3.9 8.5 - - + +
297A LEU 3.0 19.0 + - - +
298A LEU* 3.3 5.6 + - + +
300A ARG* 1.3 78.5 - - - +
302A ARG* 1.3 60.2 + - - +
304A THR* 4.0 0.4 - - - -
305A GLY 3.3 1.9 + - - -
306A THR* 2.9 46.5 + - - +
307A LEU* 3.0 36.5 + - + -
310A LEU* 4.2 0.2 - - + -
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Residues in contact with ARG 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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298A LEU 2.9 17.2 + - - +
299A VAL* 3.8 16.3 - - - +
301A ALA* 1.3 75.8 - - - +
303A ASP* 1.3 83.3 + - - +
305A GLY* 3.2 13.9 + - - -
307A LEU 3.5 13.3 - - - +
308A PRO* 4.6 8.4 - - - +
310A LEU* 3.7 28.9 - - + +
311A ASN 3.0 27.2 + - - -
312A SER* 3.9 11.4 + - - +
314A VAL* 2.8 35.8 + - + +
388A PHE 4.9 5.1 + - - -
389A VAL* 5.9 0.6 - - - +
390A TYR 5.6 1.6 - - - +
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Residues in contact with ASP 303 (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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299A VAL 3.0 16.0 + - - +
302A ARG* 1.3 106.2 + - - +
304A THR* 1.3 60.3 + - - +
305A GLY 3.3 1.5 + - - -
389A VAL* 5.6 1.4 - - - +
390A TYR* 3.3 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