Contacts of the strand formed by residues 289 - 294 (chain A) in PDB entry 4GGA
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 289 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A HIS* 3.6 7.8 - - + +
268A SER* 5.5 2.0 - - - -
284A GLY* 3.6 1.9 - - - -
285A SER* 3.1 24.3 + - - -
287A SER* 3.2 36.4 + - - +
288A GLY* 1.3 81.1 - - - +
290A ILE* 1.3 62.4 + - - +
291A HIS* 4.2 19.5 - - + +
304A THR* 4.4 6.3 - - + +
305A LEU 3.8 3.1 - - - +
306A SER* 2.6 34.8 + - - +
308A HIS 5.6 2.9 - - - -
312A VAL* 4.3 0.2 - - - +
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Residues in contact with ILE 290 (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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282A SER* 4.4 7.6 - - - -
283A SER 3.2 10.8 - - - +
284A GLY* 4.4 0.7 - - - -
289A HIS* 1.3 75.7 - - - +
291A HIS* 1.3 79.0 + - - +
292A HIS* 4.3 1.5 + - + +
303A ALA 4.1 0.2 - - - +
304A THR* 3.4 0.3 - - - +
305A LEU* 2.7 53.3 + - + +
308A HIS* 4.5 7.2 - - + -
312A VAL* 4.2 12.3 - - + -
315A LEU* 3.9 25.4 - - + -
324A LEU* 4.5 2.5 - - + -
326A SER* 3.7 31.2 - - - +
336A TRP* 3.7 27.6 - - + +
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Residues in contact with HIS 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A SER* 2.7 44.2 + - - -
267A HIS* 3.4 34.6 + + - +
281A LEU 3.7 0.9 - - - +
282A SER* 3.2 3.6 - - - -
283A SER* 2.8 36.7 + - - -
289A HIS* 4.3 8.8 - - + +
290A ILE* 1.3 82.4 - - - +
292A HIS* 1.3 63.4 + - - +
293A HIS* 3.8 10.9 - - - +
301A HIS* 3.3 34.4 + + + +
303A ALA 3.4 2.9 - - - -
304A THR* 3.7 15.3 + - + +
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Residues in contact with HIS 292 (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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280A ILE* 4.2 12.2 - - + +
281A LEU 3.7 2.2 - - - -
282A SER* 2.7 30.5 + - - -
290A ILE* 4.2 2.6 + - + -
291A HIS* 1.3 72.9 - - - +
293A HIS* 1.3 61.0 + - - +
300A HIS 3.6 0.2 - - - +
301A HIS* 3.7 5.5 - - - -
302A VAL* 3.0 36.0 + - + -
303A ALA* 3.1 34.5 + - + -
305A LEU* 3.6 24.2 - - + +
317A TRP* 3.6 22.7 - + - -
324A LEU* 3.7 16.6 - - + +
337A PRO 5.4 0.2 + - - -
345A TRP* 4.0 18.7 - + - -
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Residues in contact with HIS 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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250A VAL* 4.0 11.6 - - + +
264A MET* 4.2 28.4 - - + -
266A SER* 3.3 26.9 - - - -
267A HIS* 4.9 0.4 - + - -
280A ILE* 3.4 7.1 - - - -
281A LEU* 2.8 61.5 + - + +
283A SER* 2.7 34.7 + - - -
291A HIS* 3.8 13.9 - - + +
292A HIS* 1.3 74.4 + - - +
294A ASP* 1.3 58.9 + - - +
295A VAL* 3.3 6.0 + - + +
300A HIS* 3.2 29.0 + + + +
301A HIS* 4.5 1.2 - + - -
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Residues in contact with ASP 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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279A TYR* 3.6 12.0 - - - -
280A ILE* 4.0 12.8 - - + +
293A HIS* 1.3 68.4 - - - +
295A VAL* 1.3 60.9 + - - +
296A ARG* 3.0 53.7 + - - +
297A VAL* 3.3 40.9 + - + +
300A HIS* 2.8 19.0 + - - -
302A VAL* 4.0 17.9 - - + +
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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